Antibodies to EGF receptor epitope peptides

ABSTRACT

The present invention relates generally to growth factor receptor epitope peptides, particularly EGF family receptor epitope peptides. The invention also relates to the use of the receptor peptides in generating antibodies which have anti-tumor or anti-cancer activity or in stimulating an immunological response. The invention further relates to antibodies specifically directed against the receptor peptides. Methods for generating an immune response and for treatment of tumors and cancer are also provided.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application claims priority from co-pending U.S. ProvisionalApplication Ser. No. 60/546,602, filed Feb. 20, 2004, and Ser. No.60/584,623, filed Jul. 1, 2004, pursuant to 35 U.S.C. §119, each ofwhich is incorporated herein by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates generally to growth factor receptorepitope peptides, particularly EGF family receptor epitope peptides. Theinvention also relates to the use of the receptor peptides in generatingantibodies which have anti-tumor or anti-cancer activity or instimulating an immunological response. The invention further relates toantibodies specifically directed against the receptor peptides.

BACKGROUND OF THE INVENTION Epidermal Growth Factor Receptor (EGFR) andthe de2-7 EGFR as Targets for Therapy

Immunotherapeutic treatment of cancer has the advantage over traditionaltherapies such as surgery, radiotherapy and chemotherapy, in that therecan be a high specificity for the disease target. Tumour specific mAbscan be used to target cancer cells, creating a need to identify andlocate tumour-associated antigens as potential targets. Theoverexpression of growth factor receptors such as EGFR, IL-2 receptorand p185 HER2 is often associated with tumours such as lung, breast,head and neck, and ovarian tumours.

The EGFR belongs to a family of tyrosine kinase growth factor receptorproteins. The EGFR has long been the subject of investigation, andrecently there have been successful structure determination studiesperformed of the extracellular domains (Ogiso H et al. Cell 2002,110:775-787; Garrett T P et al. Cell 2002, 110:763-773; Ferguson K M etal Cell 2003, 11:507) and intracellular kinase domain (Stamos J et al J.Biol. Chem. 2002, 277:46265-46272). This has provided vital informationinto the behaviour of the receptor and its ligands. The EGFR is a cellsurface associated molecule, which is activated through binding ofhighly specific ligand, such as EGF and transforming growth factor alpha(TGF α). After ligand binding, the receptor dimerizes, which results inphosphorylation of the intra-cellular tyrosine kinase region. This leadsto downstream signaling, activating a cascade of responses resulting incell growth and proliferation. Given that tumour cells, unlike normalcells, are dependent on the EGFR for function, and because of the rangeof possibilities of inhibiting EGFR's regulatory control ofproliferation and differentiation in cells, the receptor is a commontarget for therapy. The EGFR is normally expressed in the liver andskin, with increased activity often found in solid tumours, such as headand neck, colorectal, pancreas, glioma, bladder and lung, thus making ita useful prognostic marker. Overexpression of the EGFR is oftenaccompanied by increased TGF α production effecting an autocrine loopgrowth advantage to the tumour. Furthermore, it was found that the EGFRgene amplification and rearrangement which is observed in some tumours,is often associated with the occurrence of mutant forms of the EGFR(Libermann T A, et al Nature 1985, 313:144-147; Wong A J, Proc Natl AcadSci USA 1992, 89:2965-2969; Frederick L, et. al Cancer Res 2000,60:1383-1387). One of the most common mutants is the EGFR variant(EGFRvIII or de2-7EGFR). The de2-7EGFR has an in-frame deletion of 801base pairs, corresponding to an over-expression of transcripts missingexons 2-7, and a sizeable deletion of amino acid residues 6-273 in theextracellular domain, with a novel glycine inserted at the splice site(Wong A J et al. Proc Natl Acad Sci USA 1992, 89:2965-2969; Sugawa N. etal Proc Natl Acad Sci USA 1990, 87:8602-8606; Yamazaki H. et al Jpn JCancer Res 1990, 81:773-779; Ekstrand A J et al Proc Natl Acad Sci USA1992, 89:4309-4313). This truncated form of the EGFR is not dependent onligand binding, and is constitutively active. The de2-7EGFR is expressedin a large fraction (>50%) of malignant gliomas and there are alsoreports linking the de2-7EGFR with breast (27%), ovarian, prostate andlung carcinomas (17%) (Wong A J, et al Proc Natl Acad Sci USA 1992,89:2965-2969; Garcia d P et al Cancer Res 1993, 53:3217-3220; WikstrandC J et al Cancer Res 1995, 55:3140-3148; Moscatello D K et al Cancer Res1995, 55:5536-5539).

Anti-EGFR Antibodies

Many studies have focused on the production of antibodies to theextracellular region of the EGFR. The mAbs generated mediate theiranti-tumour activity primarily by blocking ligand binding and also thedisruption of signaling. There were several mAbs initially developed byPeng et al. 1996 (Peng D et al Cancer Res 1996, 56:3666-3669) andMendelson et al. 1997. (Mendelsohn J Clin Cancer Res 1997, 3:2703-2707)to specifically recognize the EGFR. Mabs 425, 528 IgG2a and 225 IgG1were used to treat patients with head and neck squamous cell carcinoma(Sturgis E M, et al Otolaryngol. Head Neck Surg 1994, 111:633-643).Experimental work, including radiolabelling, has shown the mAb 425 to bean effective inhibitor of tumour growth including gliomas (Rodeck U etal J Cell Biochem 1987, 35:315-320; Brady L W et al Int J Radiat OncolBiol Phys 1991, 22:225-230; Faillot T et al Neurosurgery 1996,39:478-483). The IMC-C225 mAb specifically recognizes the EGFR, and hasmuch potential in the treatment of cancers such as head and neck,colorectal, pancreas and lung. The mAb255 up-regulates p27 K1P1 andinduces G1 arrest in a prostatic cancer cell line. Subsequently, achimeric version (ERBITUX™ (Imclone Systems, NY) IMC-C225) of the mouse225 antibody was developed to extend its therapeutic capability. TheIMC-C225 has increased binding affinity for the EGFR and is moreeffective in reducing xenograft growth in mice. Both mouse and chimericantibodies are even more effective when given in combination therapywith radiation (Robert F et al J Clin Oncol 2001, 19:3234-3243) orchemotherapy (Shin D M et al Clin. Cancer Res 2001, 7:1204-1213). Thetherapeutic mechanism of action of the IMC-C225 appears to include anefficient receptor blocking function and a capacity for ADCC. IMC-225can reduce tumour size in patients. Large doses of IMC-C225 are requiredto saturate the liver and skin binding sites and the adverse effects areprimarily acneform rash and pruitis. Clinical trials have shown partialresponse rates of tumour growth in patients of between 11% and 22% whencombined with cisplatin. The preclinical and clinical progress of thisantibody is covered in reviews by Baselga et al. [49] and Mendelsohn etal. (Baselga J et al J Clin Oncol 2000, 18:904-914; Mendelsohn J J.Clin. Oncol. 2002, 20 Suppl 1:1S-13S).

The mAb R3 was raised against the EGFR and was initially developed foruse in radioimmunotherapy (Waterfield M D, et al. J. Cell Biochem. 1982,20:149-161; Ramos-Suzarte M, et al. J. Nucl. Med. 1999, 40:768-775).Both chimeric and humanized forms of R3 have been produced and tested inAfrican Green monkeys. The humanized version of R3 retained the samebinding affinity of the mouse antibody, and was found to be 2-fold lessimmunogenic than the chimeric antibody. Preclinical studies ofxenografts in mice using technetium-labeled mouse and humanized mAbs,showed a greater potential as a diagnostic tool with the humanizedversion than the murine. The rat anti-EGFR mAb, ICR62, effectivelycompetes for ligand binding and eradicates human tumour xenografts(squamous cell carcinomas) in mice. Phase I clinical trials reported theantibody was administered safely to patients with squamous cellcarcinomas, and it has since been used to investigate the signalingpathways of growth factor receptors and their ligands in head and necksquamous cell carcinoma cell lines (O-charoenrat P et al Clin. Exp.Metastasis 2000, 18:155-161; O-charoenrat P et al. Int. J. Cancer 2000,86: 307-317; O-charoenrat P et al Oral Oncol. 2002, 38:627-640).

The anti-EGFR mAb 108.4 exhibited an anti-tumour effect that wasenhanced when combined with cisplatin (Aboud-Pirak E et al J Natl CancerInst 1988, 80:1605-1611). The same result occurred with the Fab fragmentalone, which suggests the mechanism does not rely on the interaction ofthe Fc with the host complement system. In another example, thepotential of combination therapy was investigated with the mAb RG 83852,with respect to understanding the underlying mechanism between antibodyand receptor (Perez-Soler R et al J Clin Oncol 1994, 12:730-739). It wassuggested that up-regulation of the EGFR by mAb RG 83852, increased thetyrosine kinase activity of the receptor within the tumour, thusincreasing its susceptibility to chemotherapy. Targeted irradiation bymonoclonal antibodies is another approach to cancer treatment. A numberof studies on the effect of radiolabelling several anti-EGFR antibodiesin the treatment of glioma has been undertaken by Kalofonos (Kalofonos HP et al J. Nucl. Med 1989, 30:1636-1645). These studies reported goodtargeting and minimal toxicity. The humanized mAb EMD 72000 which blocksligand binding in the EGFR is currently undergoing clinical trials (BierH et al Cancer Chemother. Pharmacol. 2001, 47:519-524). Lastly, thefully human antibody ABX-EGF derived from transgenic mice alsoeffectively targets the EGFR (Yang X D et al Crit. Rev. Oncol. Hematol.2001, 38:17-23).

Anti de2-7 EGFR Antibodies

The wild-type EGFR is expressed on most epithelial cells; so a drawbackto therapeutically targeting the receptor is the side effect of toxicityto normal tissue as well as cancer cells. Additionally, such antibodieswhen conjugated with radio-isotypes or cytotoxic agents may causepotential harm to normal tissue. Ideally it would be advantageous topreferentially target the EGFR on cancer cells. The de2-7EGFR is anattractive therapeutic target because in adults it is highly specific tocancer cells. There have been studies performed with antibodies againstthe de2-7EGFR where the inhibition of cell growth in cancer cell lineshas been shown. The mAbs 528 (Sturgis E M et al Otolaryngol. Head NeckSurg 1994, 111:633-643; Masui H et al Cancer Res 1984, 44:1002-1007) and425 (described above) bind to both the de2-7EGFR and EGFR. The uniquesequence of the de2-7EGFR generated by the insertion of a glycine at thesplice site, creates a novel epitope, located near the N-terminus of theextra-cellular region (Humphrey P A et al Proc Natl Acad Sci USA 1990,87:4207-4211; Lorimer I A et al Clin Cancer Res 1995, 1:859-864).Several antibodies, specific for the fusion junction have been produced,including mAb Y10 (Wikstrand C J et al Cancer Res. 1995, 55:3140-3148;Okamoto S et al. Br. J Cancer 1996, 73:1366-1372; Sampson J H et al.Proc Natl Acad Sci USA 2000, 97:7503-7508). This antibody, which wasused effectively to treat brain tumour xenografts in mice, functionsmechanistically by reducing cell growth, and also showed capacity forADCC and CDC. Antibodies generated against peptides of the sequencespecific for the fusion junction include the MR1, an Fv fragmentgenerated by phage display (Lorimer I A et al Proc Natl Acad Sci USA1996, 93:14815-14820). The Fv has the ability to infiltrate solidtumours, and has been used to deliver an immunotoxin. Several antibodiestargeting the fusion junction of de2-7EGFR have been radiolabelled:these include L8A4, DH8.3 and Ua30:2 (Reist C J et al Cancer Res 199757:1510-1515; Hills D et al Int J Cancer 1995, 63:537-543; Ohman L et alTumour Biol 2002, 23:61-69). The radiolabelled DH8.3 antibody recognisesthe de2-7EGFR, but not the normal EGFR, and reduces tumour size in nudemice.

The Murine Anti-EGFR Antibody mAb-806

The murine monoclonal antibody mAb-806 (class IgG2b) has been shown tobind de2-7EGFR, but not normally expressed wild-type EGFR (U.S. patentapplication U.S. Ser. No. Johns T G et al Int J Cancer 2002,98:398-408). Although mAb-806 does not react with the normal wild typereceptor, it does recognize a proportion (˜10%) of wild type EGFR ontumour cells containing amplified EGFR genes (Johns T G et al. Int JCancer 2002, 98:398-408; Luwor R B et al Cancer Res. 2001,61:5355-5361). The ability of mAb-806 to target both de2-7EGFR andamplified wild-type EGFR, both of which occur with notable frequency intumours, should confer added effectiveness for mAb-806 as a therapeuticagent.

MAb-806 differs from other antibodies that target the de2-7EGFR, in thatit does not recognize the unique fusion junction of de2-7EGFR (Wong A J,et al. Proc Natl Acad Sci USA 1992, 89:2965-2969; Sugawa N. et al. ProcNatl Acad Sci USA 1990, 87:8602-8606; Yamazaki H, et al. Jpn. J CancerRes 1990, 81:773-779; Ekstrand A J, et al. Proc Natl Acad Sci USA 1992,89:4309-4313). The binding epitope of mAb-806 exists in both the wildtype and truncated de2-7EGFR. Given the ability of mAb-806 to bind boththe de2-7EGFR and the amplified EGFR, and its absence of binding tonormally expressed wild-type receptor, it has been assumed that theepitope is conformationally dependent. Many antibodies against thewild-type EGFR in clinical development function by blocking ligandbinding. This would not appear to be the mechanism of action of mAb-806because of the characteristics of binding both with the non-ligandbinding de2-7EGFR and the amplified EGFR, and the absence of bindingwith the normal receptor. This indicates that mAb-806 does not interferewith ligand binding or dimerization.

The mAb-806 antibody binds to de2-7EGFR expressed on the U87MG.de2-7EGFRcell line, but not to the parental cell line (U87MG) which containsunamplified wild-type EGFR. In comparing the efficacy of the mAb-806with the DH8.3 mAb, it was established that mAb-806 was more efficientin tumour targeting, and had stronger binding than the DH8.3 (.EGFR(Johns T G et al Int J Cancer 2002, 98:398-408). MAb-806 was shown toinhibit the growth of mice xenografts in a dose dependent manner usingthe A431 cell line containing amplified EGFR (Johns T G et al Int JCancer 2002, 98:398-408), as well as U87MG.de2-7EGFR. Again growthinhibition was not observed in the parental U87MG xenografts.Significantly, reduced tumour growth has also been shown forintercranial xenografted glioblastomas upon application of mAb-806 toU87MG.de2-7EGFR, LN-Z308. de2-7EGFR, and A1207.de2-7EGFR xenografts (allexpressing de2-7EGFR) (Mishima K et al Cancer Res. 2001, 61:5349-5354).No significant inhibition was observed in xenografts of the parentalU87MG tumours, U87 MG.DK tumours (expressing kinase deficientde2-7EGFR), and only a small response occurs in the U87MG glioma. Areduction in angiogenesis and an increase in apoptosis occurconcurrently with the reduction in tumour growth.

With its unique properties, the mAb-806 antibody is a promisingtherapeutic for the treatment of cancers such as head and neck cancer,and glioma. The development of a humanized form of mAb-806 will have amajor effect on its efficacy. Such an antibody should avoid a HAMAresponse, improve its ability to recruit effector function and increaseits half-life in circulation, thus greatly enhancing its clinicalprospects.

Initially there were high expectations for the use of mAbs astherapeutic magic bullets, but it was soon realised that there areseveral major impediments limiting the clinical use of non-humanantibodies. The administration of multiple doses of non-human mAbsgenerally provokes an unwanted immune response thus severely limitingtheir use as a therapeutic. The mouse antibody is recognized by thehuman immune system as a foreign protein resulting in an immune effectknown as the human anti-mouse antibody response, i.e. the HAMA response.The HAMA response can result in neutralization of the antibody functionand in serious allergic-like reactions.

Much of the HAMA response is directed against the antigen bindingportion (Fab) and rarely the constant regions (Fc) of the antibody.Additional problems resulting from the clinical application of rodentmAbs are associated with the Fc regions. The human Fc binds tospecialised Fc receptors, which help to maintain the antibodies incirculation. As a result, rodent mAbs have a shortened half-life,usually 1-3 days as compared with a week or more for human Ig. Anotherlimitation is the reduced recruitment of a variety of effector functionsinitiated on binding of the Fc to the human Fc receptor. The binding toFc receptors of specialized effector cells such as macrophages,monocytes and neutrophils, triggers the immune system leading to aresponse known as antibody-dependent cell-mediated cytolysis (ADCC). Fcreceptors are also responsible for the triggering of the complementcascade (a group of interacting proteins) leading to thecomplement-dependent cytolysis response (CDC). This results in celllysis and increases the effectiveness of antibodies to fight bacterialinfection. The class of the constant domains predominantly controls theefficacy of the antibody in cell lysis.

There are different approaches that may be taken to overcome theimmunogenicity of mouse mAbs, such as rapid infusion of antibody doseand the use of antibody fragments (e.g. single chain Fv (scFv) seeCarter P Nat. Rev. Cancer 2001, 1:118-129; Hudson P et al Nature Med2003, 9:129-134 and references therein). Alternatively, antibodyengineering methods have been employed to reduce the HAMA response whenwhole IgGs are used for therapy.

This approach has the added potential advantages of increasing half-lifeand more effective recruitment of effector function. Such humanizationmethods are well known within the art and have for example beendescribed in U.S. Pat. Nos. 5,225,539, 5,530,101, 5,585,089, 5,859,205,and 6,797,492 each incorporated herein by reference.

Human Antibodies

An alternative approach to overcoming the problem of immunogenicity inmAbs is the production of completely (fully) human antibodies. Phagedisplay technology can be used to select a range of human antibodiesbinding specifically to the antigen using methods of affinity enrichment(McCafferty J et al Nature 1990, 348:552-554; Azzazy H M et al Clin.Biochem. 2002, 35:425-445). The bacteriophage is a virus that onlyinfects bacteria, and reproduces in Escherichia coli. The phage displayprocess involves the insertion of human genetic material into the phagegenome. The filamentous phage system has the unique property where thestructural and functional information of the ligand displayed on thephage surface (phenotype) is linked to the ligand's genetic informationwithin the phage genome (genotype). Therefore, a library of Ig moleculescan be generated and displayed on the surface of filamentous phage, andthose showing binding affinities are selected. This method has theadvantage of a very rapid simultaneous screening of many antibodies withhigh antigen affinity. It has also been used successfully in antibodyhumanizations by generating a combinatorial library including a set ofpotentially critical residues needed to preserve full binding avidity.The framework can then be optimised by random mutagenesis of thecritical residues.

Transgenic Mice

Recently, an alternative approach to phage display methodology ofproducing human mAbs was developed where the human genes are insertedinto the mouse DNA creating transgenic mice, capable of generating fullyhuman protein sequences (for reviews of the methods involved, seereferences Little M et al Immunol. Today 2000, 21:364-370; Humphreys D Pet al Curr. Opin. Drug Discov. Devel. 2001, 4:172-185; Ishida T et alNippon Rinsho 2002, 60:439-444). Accordingly, these mice can producehuman antibodies in response to immunization with a target antigen. Theantibodies generated are effectively human and would not be expected tobe rejected by the host immune system. The XenoMouse® produced byAbgenix contains approximately 80% of the human heavy chain genes, and alarge number of light chain genes. Different strains of the mice havebeen produced containing different classes of antibodies capable oftargeting a range of diseases (Yang X D et al Cancer Res 1999,59:1236-1243; Davis C G et al Cancer Metastasis Rev 1999, 18:421-425).For example, ABX-MA1 is a fully human antibody which targets MCAM/MUC18(a glycoprotein associated with tumour thickness and metastases in humanmelanoma cells in mice) and shows promise in the treatment of melanoma(Mills L et al Cancer Res 2002, 62:5106-5114). ABX-EGF targets the EGFR,and is currently in phase I/II clinical trial in the treatment of headand neck, non-small cell lung carcinoma, and colon cancer.

Therefore, in view of the aforementioned deficiencies attendant withprior art methods and the recognition of the usefulness and applicationof antibodies in the diagnosis, treatment, and prevention of disease, itshould be apparent that there still exists a need in the art for apreparation and use of humanized/fully human antibodies, particularlydirected against the EGF receptor. There is a particular need forhumanized/fully human antibodies which demonstrate reduced or absence ofantibody immune response in humans and that recognize oncogenic oractivated forms of EGFR as well as amplified or overexpressed forms ofEGFR.

The citation of references herein shall not be construed as an admissionthat such is prior art to the present invention.

SUMMARY OF THE INVENTION

In accordance with the present invention, and to elucidate the mechanismleading to the unique specificity and mode of anti-tumor activity of theEGFR antibody mAb806, the EGFR binding epitope of mAb 806 has beendetermined. The epitope receptor peptide, CGADSYEMEEDGVRKC (SEQ IDNO: 1) contains the mAb806 epitope. The receptor peptide is suitable forgenerating EGFR antibodies which are capable of recognizing EGFR whichis found in tumorigenic, hyperproliferative or abnormal cells and is notdetectable or transitional in normal or wild type cells (the term “wildtype cell” as used herein contemplates a cell that expresses endogenousEGFR but not the de 2-7 EGFR and the term specifically excludes a cellthat overexpresses the EGFR gene; the term “wild type” refers to agenotype or phenotype or other characteristic present in a normal cellrather than in an abnormal or tumorigenic cell).

Thus, the invention provides receptor epitopes, particularly growthfactor receptor epitopes, which can be utilized in generating antibodieswhich have anti-tumor capacity and activity or stimulating animmunological response which is an anti-tumor response. The growthfactor receptor epitopes include loop epitopes that are exposed intransitional forms of the growth factor receptor and are capable ofgenerating antibodies which recognize transitional forms of thereceptor, thereby modulating, including preventing or inhibiting, theiractivation, including the change from an inactive to active ligand-boundconformation. The invention provides receptor epitopes, particularly EGFfamily receptor epitopes, most particularly EGFR epitopes, which can beutilized in generating antibodies which have anti-tumor capacity andactivity or stimulating an immunological response which is an anti-tumorreponse. In a general aspect the invention provides a receptor epitope,particularly an EGF receptor epitope or EGF receptor family epitope,which is found in tumorigenic, hyperproliferative or abnormal cells andis not detectable or transitional in normal or wild type cells.

In accordance with the present invention, growth factor receptorpeptides, particularly EGFR peptides are provided which are capable ofgenerating antibodies, particularly monoclonal antibodies, which haveanti-tumor activity.

In accordance with the present invention, growth factor receptorpeptides, particularly EGFR peptides are provided which are capable ofgenerating antibodies which are capable of recognizing EGFR which isfound in tumorigenic, hyperproliferative or abnormal cells and is notdetectable or transitional in normal or wild type cells.

The growth factor receptor peptides, particularly the EGF familyreceptor peptides, of the present invention provide diagnostic andtherapeutic uses to identify, characterize and target a number of tumortypes, for example, head and neck, breast, lung, bladder, colon orprostate tumors and glioma, without the problems associated with normaltissue uptake that may be seen with previously known growth factorreceptor, including EGFR, antibodies.

In its broadest aspect, the present invention encompasses isolatedpolypeptides comprising an amino acid sequence of a growth factorreceptor peptide having an amino acid sequence selected from any of SEQID NOS: 1-14. The isolated peptides, including combinations of one ormore thereof, are suitable for use in generating antibodies whichrecognize growth factor receptor and have anti-tumor activity and inimmunizing animals, particularly mammals, most particularly humans, whohave cancer or tumor disease.

The present invention is directed to an isolated receptor polypeptidewhich comprises the amino acid sequence set out in any of SEQ ID NOS:1-14 and immunogenic fragments thereof.

The invention provides an isolated peptide having the amino acidsequence CGADSYEMEEDGVRKC (SEQ ID NO: 1).

The invention provides an isolated peptide having the amino acidsequence CGADSYEMEEDGVRK (SEQ ID NO: 2).

The invention provides an isolated peptide having the amino acidsequence CGPDYYEVEEDGIRKC (SEQ ID NO: 3).

The invention provides an isolated peptide having the amino acidsequence CNTDTYEVEENGVRKC (SEQ ID NO: 4).

The invention provides an isolated peptide having the amino acidsequence CGPDSYEVEEDGVRKC (SEQ ID NO: 5).

The invention provides an isolated peptide having the amino acidsequence CSSDSYEVEEDGVRKC (SEQ ID NO: 6).

The invention provides an isolated peptide having the amino acidsequence CGADSYEMEEDAVRKC (SEQ ID NO: 7).

The invention provides an isolated peptide having the amino acidsequence CPLHNQEVTAEDGTQRC (SEQ ID NO: 8).

The invention provides an isolated peptide having the amino acidsequence CPPDKMEVDKNGLKMC (SEQ ID NO: 9).

The invention provides an isolated peptide having the amino acidsequence CPSSKMEVEENGIKMC (SEQ ID NO: 10).

The invention provides an isolated peptide having an amino acidsequence:

C X₁ X₂ X₃ X₄ X₅ X₆ X₇ X₈ X₉ X₁₀ X₁₁ X₁₂ X₁₃ X₁₄ X₁₅

wherein each X_(n) residue can be independently selected as follow (SEQID NO: 11):

X₁ is G, P, N or S;

X₂ is A, P, T, S or L;

X₃ is D, H or S;

X₄ is S, Y, T, N or K;

X₅ is Y, Q or M;

X₆ is M or V;

X₇ is E, T or D;

X₈ is A or none;

X₉ is E or K;

X₁₀ is D or N;

X₁₁ is G or A;

X₁₂ is V, I, L or T;

X₁₃ is R, Q or K;

X₁₄ is R, K or M;

X₁₅ is C or none.

The invention provides an isolated peptide having an amino acidsequence:

C X₁ X₂ X₃ X₄ X₅ X₆ X₇ X₈ X₉ X₁₀ X₁₁ X₁₂ X₁₃ X₁₄ X₁₅

wherein each X_(n) residue can be independently selected as follows (SEQID NO: 12):

X₁ is G, P, N, Q, S or T

X₂ is A, P, T, S, L, M, V, I or P

X₃ is D, E, H, R, K, S or T

X₄ is S, Y, F, W, T, N, Q, K or R

X₅ is Y, F, W, Q, N, M, V, A, L, I or P

X₆ is M, V, A, L, I or P

X₇ is E, D, T or S

X₈ is A, V, L, I, P, M or none

X₉ is D, E, K or R

X₁₀ is D, E, N or Q

X₁₁ is G, A, M, V, L, I or P

X₁₂ is V, I, L, M, A, P, S or T

X₁₃ is R, K, H, Q or N

X₁₄ is R, K, H, M, A, V, L, I or P

X₁₅ is C or none.

The invention provides an isolated peptide having an amino acidsequence:

C X₁ X₂ X₃ X₄ X₅ E X₆ X₇ X₈ X₉ G X₁₀ X₁₁ X₁₂ C

wherein each X_(n) residue can be independently selected as follows (SEQID NO: 13):

X₁ is G or A

X₂ is A or K

X₃ is D or A

X₄ is S or A

X₅ is Y or A

X₆ is M or A

X₇ is E or A

X₈ is E or A

X₉ is D or A

X₁₀ is V, A or K

X₁₁ is R or A

X₁₂ is K or A.

The invention provides an isolated peptide having the amino acidsequence

C X₁ X₂ X₃ X₄ X₅ E X₆ X₇ X₈ DGVRKC

wherein each X_(n) residue can be independently selected as follows (SEQID NO: 14):

X₁ is G or A

X₂ is A or K

X₃ is D or A

X₄ is S or A

X₅ is Y or A

X₆ is M or A

X₇ is E or A

X₈ is E or A.

The present invention further provides an isolated nucleic acid whichencodes the peptide set out in any of SEQ ID NOS: 1-14.

The present invention extends to an immunogenic receptor peptide,particularly selected from any of SEQ ID NOS: 1-14, or an immunogenicfragment thereof. The present invention also extends to immunogenicreceptor peptides wherein such polypeptides comprise a combination of atleast one immunogenic receptor peptide, selected from any of SEQ ID NOS:1-14, or immunogenic peptide fragment thereof.

The invention provides a method for immunizing a mammal comprisingadministering an growth factor receptor epitope peptide or animmunogenic fragment thereof, whereby antibodies which areimmunoreactive with the epitope peptide exposed on cells expressingabnormal or overexpressed growth factor receptor, but not exposed onwild type cells, are produced. The invention further provides a methodfor immunizing a mammal comprising administering an EGF receptor peptideselected from any of SEQ ID NOS: 1-14 or an immunogenic fragmentthereof, whereby antibodies which are immunoreactive with the epitopepeptide exposed on cells expressing abnormal or overexpressed EGFR, butnot exposed on wild type cells, are produced. The invention provides amethod for immunizing a mammal comprising administering an EGF receptorpeptide selected from any of SEQ ID NOS: 1-14 or an immunogenic fragmentthereof, whereby antibodies which are immunoreactive with the EGFreceptor epitope peptides are produced.

In a further aspect, the present invention extends to vaccines andimmunogenic compositions based on the receptor peptides describedherein. The present invention provides a vaccine comprising one or moreEGFR peptide selected from any of SEQ ID NOS: 1-14, and apharmaceutically acceptable adjuvant. The present invention provides avaccine comprising one or more peptides selected from any of SEQ ID NOS:1-14, and a pharmaceutically acceptable adjuvant. The present inventionprovides an immogenic composition comprising one or more EGFR peptideselected from any of SEQ ID NOS: 1-14, and a pharmaceutically acceptableadjuvant. The present invention provides an immunogenic compositioncomprising one or more peptides selected from any of SEQ ID NOS: 1-14,and a pharmaceutically acceptable adjuvant.

The present invention further provides an anti-tumor or anti-cancervaccine comprising one or more EGF family receptor peptides selectedfrom the group of any of SEQ ID NOS: 1-14, further comprising one ormore additional tumor antigens. The present invention further provides atumor or anti-cancer vaccine comprising one or more EGF family receptorpeptides selected from the group of any of SEQ ID NOS: 1-14, furthercomprising one or more additional EGF or EGFR antigens.

In another aspect, the invention is directed to a vaccine for treatmentof a mammal, particularly a human, subject suffering from head and neckcancer, breast cancer, lung, bladder, colon or prostate tumors andglioma, or any other tumour showing aberrant expression of EGFR (or anyof the EGFR family of receptors) comprising an immunogenic amount of oneor more EGF family receptor peptides selected from the group of any ofSEQ ID NOS: 1-14 or immunogenic fragment thereof. Such a vaccine maycontain the peptide and a pharmaceutically acceptable adjuvant. Such avaccine may further contain the peptide conjugated to a carrier.

The invention provides pharmaceutical compositions comprising an EGFfamily receptor loop peptide and a pharmaceutically acceptable carrier.The invention provides pharmaceutical compositions comprising an EGFfamily receptor peptide selected from one or more of peptides selectedfrom any of SEQ ID NOS: 1-14, and a pharmaceutically acceptable carrier.The invention provides pharmaceutical compositions comprising an EGFfamily receptor loop peptide antibody and a pharmaceutically acceptablecarrier. The invention provides pharmaceutical compositions comprisingan EGF family receptor peptide antibody immunoreactive with one or moreof peptides selected from any of SEQ ID NOS: 1-14, and apharmaceutically acceptable carrier.

In a still further aspect, the present invention provides a purifiedantibody to an EGF family receptor peptide selected from any of SEQ IDNOS: 1-14.

Antibodies against the isolated polypeptides of the present inventioninclude naturally raised and recombinantly prepared antibodies. Thesemay include both polyclonal and monoclonal antibodies prepared by knowngenetic techniques, as well as bi-specific antibodies, and antibodiesincluding other functionalities suiting them for diagnostic ortherapeutic use. Such antibodies can be used in immunoassays tocharacterize tumors or diagnose cancer including, but not limited to,head and neck cancer, breast cancer, lung cancer, ovarian cancer,bladder cancer, laryngeal cancer, squamous cell carcinoma, or prostatetumors and glioma. The antibodies can also be used for passiveimmunization to reduce tumors or treat cancer including, but not limitedto, head and neck cancer, breast cancer, lung cancer, ovarian cancer,bladder cancer, laryngeal cancer, squamous cell carcinoma, or prostatetumors and glioma.

An antibody to an EGF family receptor peptide selected from any of SEQID NOS: 1-14 labeled with a detectable label is further provided. Inparticular embodiments, the label may selected from the group consistingof an enzyme, a chemical which fluoresces, and a radioactive element. Inthe instance where a radioactive label, such as the isotopes ³H, ¹⁴C,³²P, ³⁵S, ³⁶Cl, ⁵¹Cr, ⁵⁷Co, ⁵⁸Co, ⁵⁹Fe, ⁸⁶Y, ⁹⁰Y, ¹²⁴I, ¹²⁵I, ¹³¹I,¹¹¹I, ⁹⁹Tc and ¹⁸⁶Re are used, known currently available countingprocedures may be utilized. In the instance where the label is anenzyme, detection may be accomplished by any of the presently utilizedcolorimetric, spectrophotometric, fluorospectrophotometric, amperometricor gasometric techniques known in the art.

The present invention provides a pharmaceutical composition comprisingone or more antibodies to an EGF family receptor peptide selected fromany of SEQ ID NOS: 1-14, and a pharmaceutically acceptable carrier. Theinvention further provides a pharmaceutical composition comprising acombination of at least two antibodies to an EGF family receptor peptideselected from any of SEQ ID NOS: 1-14 and a pharmaceutically acceptablecarrier.

In a further embodiment, the present invention relates to certaintherapeutic methods which would be based upon the activity of anantibody, or active fragments thereof, to an EGF family receptor peptideselected from any of SEQ ID NOS: 1-14, or upon agents or other drugsdetermined to possess the same activity. A first therapeutic method isassociated with the prevention or treatment of cancer, including but notlimited to head and neck, lung, colon, bladder breast, prostate andglioma.

In particular, the antibodies of the present invention, or activefragments thereof, and chimeric or synthetic antibodies derivedtherefrom can be prepared in pharmaceutical compositions, including asuitable vehicle, carrier or diluent, for administration in instanceswherein therapy is appropriate, such as to treat cancer. Suchpharmaceutical compositions may also include methods of modulating thehalf-life of the binding members, antibodies or fragments by methodsknown in the art such as pegylation. Such pharmaceutical compositionsmay further comprise additional antibodies or therapeutic agents.

Thus, a composition of the present invention may be administered aloneor in combination with other treatments, therapeutics or agents, eithersimultaneously or sequentially dependent upon the condition to betreated. In addition, the present invention contemplates and includescompositions comprising antibodies to an EGF family receptor peptideselected from any of SEQ ID NOS: 1-14, particularly antibody or fragmentthereof, herein described and other agents or therapeutics such asanti-cancer agents or therapeutics, anti-EGFR agents or antibodies, orimmune modulators. More generally these anti-cancer agents may betyrosine kinase inhibitors, such as AG1478, ZD1839 (gefitinib) or ST1571(imatinib mesylate) phosphorylation cascade inhibitors,post-translational modulators, cell growth or division inhibitors (e.g.anti-mitotics), PDGFR inhibitors or signal transduction inhibitors.Other treatments or therapeutics may include the administration ofsuitable doses of pain relief drugs such as non-steroidalanti-inflammatory drugs (e.g. aspirin, paracetamol, ibuprofen orketoprofen) or opiates such as morphine, or anti-emetics. Thus, theseagents may be anti-EGFR specific agents, such as AG1478 or ZD1839, ormay be more general anti-cancer and anti-neoplastic agents, non limitingexamples including doxorubicin, carboplatin and cisplatin. In addition,the composition may be administered with immune modulators, such asinterleukins, tumor necrosis factor (TNF) or other growth factors,cytokines or hormones such as dexamethasone which stimulate the immuneresponse and reduction or elimination of cancer cells or tumors. Thecomposition may also be administered with, or may include combinationsalong with other anti-EGFR antibodies, including but not limited to theanti-EGFR antibodies 528; 225; SC-03; 108 (ATCC HB9764) U.S. Pat. No.6,217,866; 14E1 (U.S. Pat. No. 5,942,602); DH8.3; L8A4; Y10; HuMAX-EGFr(Genmab/Medarex); ICR62; and ABX-EGF (Abgenix).

The present invention also includes antibodies to an EGF family receptorpeptide selected from any of SEQ ID NOS: 1-14, and any fragmentsthereof, which are covalently attached to or otherwise associated withother molecules or agents to be used for therapeutic or diagnosticpurposes. These other molecules or agents include, but are not limitedto, molecules (including other antibodies or antibody fragments) withdistinct characteristics, toxins, ligands, radioactive isotopes andchemotherapeutic agents. Within the are there are many well-knownmolecules or agents which have been covalently linked or otherwiseassociated to antibodies to be used for therapeutic purposes. Examplesof such molecules or agents include, but are not limited to: toxins suchas calicheamicin, maytansinoid, duocarmycin, ricin, diphtheria toxin andpseudomonas exotoxin; ligands such as tumor necrosis factor (TNF);radioactive isoptopes such as ⁹⁰Y, ¹²⁵I, ¹³¹I, ²¹¹At, ²²⁵Ac, ²¹³Bi andother α, β or γ emitting isotope; and chemotherapeutic drugs aspaclitaxel (Taxol®) and doxorubicin (Adriamycin®).

The present invention contemplates the use of the receptor peptides andantibodies thereto of the present invention in diagnostic tests andmethods for determining and/or monitoring tumors and cancer includinghead and neck cancer, breast cancer, lung cancer, ovarian cancer,bladder cancer, laryngeal cancer, squamous cell carcinoma, or prostatetumors and glioma.

The present invention also relates to isolated nucleic acids, such asrecombinant DNA molecules or cloned genes, or degenerate variantsthereof, mutants, analogs, or fragments thereof, which encode theisolated growth factor receptor peptide of the present invention orwhich competitively inhibit the activity of the polypeptide. The presentinvention further relates to isolated nucleic acids, such as recombinantDNA molecules or cloned genes, or degenerate variants thereof, mutants,analogs, or fragments thereof, which encode an EGF family receptorpeptide selected from any of SEQ ID NOS: 1-14. In a further embodimentof the invention, the DNA sequence of the recombinant DNA molecule orcloned gene may be operatively linked to an expression control sequencewhich may be introduced into an appropriate host. The inventionaccordingly extends to unicellular hosts transformed with therecombinant DNA molecule comprising a DNA sequence encoding an EGFfamily receptor peptide selected from any of SEQ ID NOS: 1-14.

A nucleic acid capable of encoding an EGF family receptor peptideselected from any of SEQ ID NOS: 1-14, which is a recombinant DNAmolecule is further provided. Such a recombinant DNA molecule whereinthe DNA molecule is operatively linked to an expression control sequenceis also provided herein.

The present invention relates to nucleic acid vaccines or DNA vaccinescomprising nucleic acids encoding immunogenic EGF family receptorpeptides, particularly selected from any of SEQ ID NOS: 1-14. Thepresent invention relates to nucleic acid vaccines or DNA vaccinescomprising nucleic acids encoding one or more immunogenic an EGF familyreceptor peptide selected from any of SEQ ID NOS: 1-14 with at least oneother polypeptide, particularly a tumor antigen or immunomodulatorymolecule peptide.

The present invention provides a vector which comprises the nucleic acidcapable of encoding encoding an EGF family receptor peptide selectedfrom any of SEQ ID NOS: 1-14 and a promoter. The invention contemplatesa vector wherein the promoter comprises a bacterial, yeast, insect ormammalian promoter. The invention contemplates a vector wherein thevector is a plasmid, cosmid, yeast artificial chromosome (YAC),bacteriophage or eukaryotic viral DNA.

The present invention further provides a host vector system for theproduction of a polypeptide which comprises the vector capable ofencoding an EGF family receptor peptide selected from any of SEQ ID NOS:1-14 in a suitable host cell. A host vector system is provided whereinthe suitable host cell comprises a prokaryotic or eukaryotic cell. Aunicellular host transformed with a recombinant DNA molecule or vectorcapable of encoding an EGF family receptor peptide selected from any ofSEQ ID NOS: 1-14 is thereby provided.

The present invention includes methods for determining and monitoringtumors and cancer including head and neck cancer, breast cancer, orprostate tumors and glioma by detecting the presence or exposure of anEGF receptor epitope peptide selected from the group of any of SEQ IDNOS: 1-14. In a particular such method, the EGF receptor epitope peptideis measured by:

-   -   a. contacting a sample in which the presence or exposure of an        EGF receptor epitope peptide selected from the group of any of        SEQ ID NOS: 1-14 is suspected with an antibody to the said EGF        receptor peptide under conditions that allow binding of the        peptide to the antibody to occur; and    -   b. detecting whether binding has occurred between the EGF        receptor epitope peptide from the sample and the antibody;        wherein the detection of binding indicates the presence or        exposure of the EGF receptor epitope peptide in the sample.

The invention includes an assay system for screening of potentialcompounds effective to modulate the exposure of an EGF receptor epitopepeptide of the present invention or the stability of an EGFRtransitional state. In one instance, the test compound, or an extractcontaining the compound, could be administered to a cellular sampleexpressing the particular EGFR to determine the compound's effect uponthe exposure of an EGF receptor epitope peptide of the present inventionor the stability of an EGFR transitional state by comparison with acontrol.

It is still a further object of the present invention to provide amethod for the treatment of mammals suffering from tumors or cancerincluding head and neck cancer, breast cancer, lung cancer, ovariancancer, bladder cancer, laryngeal cancer, squamous cell carcinoma, orprostate tumors and glioma.

The invention provides a method for the treatment of mammals sufferingfrom tumors or cancer including head and neck cancer, breast cancer,lung cancer, ovarian cancer, bladder cancer, laryngeal cancer, squamouscell carcinoma, or prostate tumors and glioma comprising administeringan immunogenically effective dose of a vaccine comprising an EGFreceptor epitope peptide selected from the group of any of SEQ ID NOS:1-14 to a subject.

In a further aspect, the invention provides a method of inducing animmune response in a subject which has tumors or cancer including headand neck cancer, breast cancer, lung cancer, ovarian cancer, bladdercancer, laryngeal cancer, squamous cell carcinoma, or prostate tumorsand glioma comprising administering to the subject an amount of thepharmaceutical composition comprising an EGF receptor epitope peptideselected from the group of any of SEQ ID NOS: 1-14, and apharmaceutically acceptable carrier, thereby inducing an immuneresponse.

Other objects and advantages will become apparent to those skilled inthe art from a review of the following description which proceeds withreference to the following illustrative drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Reactivity of mAb 806 with fragments of the EGFR. Solublefragments of the EGFR (1-513 and 310-501) or cell lysates containinggrowth hormone/EGFR fragment fusion proteins (GH-274-501, GH-282-501,GH-290-501 and GH-298-501) were separated by SDS-PAGE, transferred tomembrane and immunoblotted with mAb 806 (left panel) or the anti-mycantibody 9B 11 (right panel).

FIG. 2A-2B. Reactivity of mAb 806 with fragments of the EGFR displayedon yeast. A, Representative flow cytometry histograms depicting the meanfluorescence signal of mAb 806 labeling of yeast displayed EGFRfragments. With yeast display a percentage of cells do not expressproteins on their surface resulting in 2 histogram peaks. mAb 806 didnot bind to the uninduced negative control B, The 1-501 EGFR fragmentwas denatured by heating yeast pellets to 80° C. for 30 min. The linearc-myc C-terminal tag on the 1-501 fragment was still recognized by the9E10 antibody, demonstrating that heat treatment does not comprise theyeast surface displayed fragment. The conformation sensitive mAb 225 wasused to confirm denaturation.

FIG. 3A-3B. Inhibition of mAb 806 binding with an EGFR derived peptide.A, The 1-501 and GH-274-501 EGFR fragments were immunoblotted with mAb806 (upper panels) as described in FIG. 1 in the presence or absence ofthe 287-302 EGFR peptide. Presence of EGFR fragments was confirmed aftermAb 806 immunoblotting by stripping membranes and re-probing withanti-myc (lower panels). B, ELISA plates were coated with the 1-501 EGFRfragment and then incubated with mAb 806 in the presence of increasingconcentrations of the 287-302 (CGADSYEMEEDGVRKC (SEQ ID NO:1)) or287-298 (CGADSYEMEEDG (SEQ ID NO: 15)) EGFR peptides. Data are expressedas mean A₄₀₅±SD.

FIG. 4A-4B. Inhibition of mAb 806 binding with chemical modified 287-302EGFR peptide. A, ELISA plates were coated with 501-Fc and then incubatedwith mAb 806 in the presence of increasing concentrations of oxidized,reduced and aged (prepared as described in Experimental Procedures)287-302 EGFR peptide. Data are expressed as mean percentage inhibition±SD (error bars are too small to be visible). B, ELISA plates werecoated with 501-Fc and then incubated with mAb 806 in the presence ofincreasing concentrations of S-carboxymethylated 287-302 EGFR peptide orthe N-terminal (CGADSYEM) (SEQ ID NO: 16) and C-terminal (EEGVRKC) (SEQID NO: 17) peptides created from the CNBr cleavage of the 287-302 EGFRpeptide. Data are expressed as mean percentage inhibition ±SD (errorbars are too small to be visible).

FIG. 5A-5B. Analysis of mAb 806 binding to peptides by BIAcore. A, The287-302 EGFR peptide was immobilized on the surface by thiol couplingand the mAb 806 antibody passed over at increasing concentrations(31.25, 62.5, 125, 250, 500 and 1000 nM). Binding affinity was thendetermined by Scatchard analysis (insert). B, The 287-302 EGFR peptidewas immobilized on the surface by amine coupling and the mAb 806antibody at a concentration of 500 nM was passed over the surface in thepresence of the 287-302 (upper panel), 287-298 (middle panel) or 287-301(lower panel) EGFR peptides (5 and 10 μM).

FIG. 6A-6D. Location of the mAb 806 epitope within the EGFR structure.A, Carbon trace showing the structure of the cysteine loop containingthe mAb 806 epitope. B, Space-filled model of the ligand-bound dimericform of the EGFR. The dimer is predominantly stabilized by the twodimerization arms located in the CR1-loop of each EGFR molecule C,Tethered form of the EGFR showing the auto-inhibitory interactionbetween domains CR1 and CR2, which prevents dimerization. D, Extended(transitional) form of the EGFR clearly showing the dimerization arm(left figure) of the CR1-loop poised and ready for interaction with asecond loop on an adjacent molecule. Colors: EGF ligand is shown inorange; glycosylation site at amino acid 579 red and mAb 806 epitope inpurple. EGFR structures (31, 35, 36) and a possible receptor activationmechanism have been described in detail previously.

FIG. 7. Flow cytometry analysis of 293T cells expressing CR1-loopdeletions of the EGFR. Parental 293 cells, which express low amounts ofendogenous wild type EGFR, were transfected with the de2-7 EGFR or thedeCR1-loop EGFR (2 independent clones) and stained with either anirrelevant IgG2b antibody (open histograms), mAb 528 (black histograms)or mAb 806 (grey histograms).

FIG. 8A-8C. A, Possible anti-tumor mechanism of mAb 806. The mAb 806cannot bind the inactive EGFR but as the receptor untethers the mAb 806epitope becomes exposed allowing the antibody to bind. Binding of mAb806 to the receptor would almost certainly prevent dimerization, andhence EGFR signalling, and may induce EGFR internalization. B, Homologyof the mAb 806 containing cysteine loop in ErbB3 and ErbB4. Amino acidsconserved in ErbB1 are shown in red and residues displaying conservationof charge are shown in green. C, The CR1-CR2 dimer interface. The firstcarbohydrate moiety attached to N579 is clearly visible in the crystalstructure and is located at the CR1-CR2 dimer interface. In cellsover-expressing the EGFR, this site is only glycosylated 80% of thetime. Differences in glycosylation may effect the dynamics of tetheringand hence mAb 806 reactivity.

FIG. 9A-9B. A) Schematic representation of hEGFR domain structure and ofthe mutations constructed for this study. Abbreviations: L, Ligandbinding domains; CR, cysteine-rich domains; JM, juxtamembrane domain;C-T, carboxy-terminal domain. B) Upper panel: Ribbon diagrams of theuntethered, dimeric form of the EGFR ECD (1-501) in complex with TGFα(from Garrett et al., 2002). The EGFR molecules are colored in blue andgreen; the bound TGFα molecules are colored purple. The epitope formAb806 (described later) is colored pink. Lower panel: Ribbon diagram ofthe tethered form of the EGFR ECD (1-621) (from Ferguson et al., 2003).The CR2 domain (aa 501-621) is shown in yellow. In both panels theinserts highlight the interactions between CR1-loops of the untetheredconformation or between the CR1-loop and the CR2 domain in theuntethered conformation. The amino acids mutated in the constructs areshown in the inserts. Atoms in close van der Waals contact are connectedby dotted lines, and the H-bonds are represented by dashed lines.

FIG. 10. FACS analysis of BaF/3 cell lines stably expressing wt ormutant EGFR. Cells were incubated with mAb528 followed byAlexa488-labelled anti-mouse Ig as detailed in Experimental Procedures.The plots represent fluorescence intensity on the abscissa and cellnumber per fluorescence channel on the ordinate. The negative control(irrelevant antibody) fluorescence is plotted on each panel as lightgrey overlay.

FIG. 11. Scatchard analysis of EGF binding to wt and mutant receptors.Ligand binding affinities were determined at a fixed concentration of¹²⁵I-EGF by competition with unlabelled EGF (see ExperimentalProcedures). The plots were generated from the raw data using the “Kellfor Windows” version of the RadLig program (BioSoft).

FIG. 12A-12C. Dimerization of WT and mutant EGFRs, and specificphosphotyrosine content of receptor complexes. Quiescent cells weretreated with EGF (100 ng/ml, 16 nM) or control buffer. Thehomobifunctional, cell-impermeable cross-linker BS³ was addedimmediately, and the incubation continued for 30 min at roomtemperature. After quenching the reaction, the cells were lysed,cellular proteins separated by SDS/PAGE and transferred to PVDF membranefor immunoblotting. A) Immunodetection of EGFR protein (top) andphosphotyrosine (bottom). The PVDF membrane was stripped after exposureto the anti-phosphotyrosine antibody and re-probed with the anti-EGFRantibody. B) Ratios of dimer to total EGFR (dimer+monomer) with andwithout EGF stimulation, determined by quantitative scanningdensitometry as described in Experimental Procedures. C) Ratios ofphosphotyrosine content to EGFR monomer and dimer protein, determined byquantitative scanning densitometry as above.

FIG. 13A-13C. Ligand-dependent tyrosine phosphorylation and MAPKactivation. A) Quiescent cells were exposed to EGF (100 ng/ml) for 10min. at room temperature, then lysed directly in SDS-PAGE sample buffer.Proteins were separated on 4-12% gels, transferred to PVDF membranes andprobed with antibodies to phosphotyrosine (top) or to phospho-MAPK(bottom). The blots were stripped and reprobed with anti-EGFR antibodiesor anti-MAPK antibodies respectively (not shown) to allow thedetermination of specific protein phosphorylation as described inExperimental procedures. B) Ratios of phosphotyrosine to EGFR proteinfor wt and mutant receptors. C) Ratio of phospho-MAPK to total MAPKprotein.

FIG. 14A-14C. Dose-response of EGFR activation in CR2 mutants. Cellsexpressing the wt or CR2-mutant receptors were rendered quiescent bygrowth factor and serum withdrawal, then exposed to control buffer or toincreasing concentrations of EGF (0.03 to 100 nM). A): total celllysates were analyzed by SDS/PAGE on 4-12% gradient gels, followed byimmunoblotting with anti-phosphotyrosine, anti-EGFR or anti-phospho-MAPKantibodies. B) and C): the films were scanned for densitometricquantitation of the reactive bands and the phospho-Shc and phospho-MAPKdata were plotted as % maximal band intensity against EGF concentration.Symbols are: closed circles, wtEGFR; dark triangles, D⁵⁶³H-EGFR; lighttriangles, V⁵⁸³D-EGFR; open squares, E⁵⁷⁸C-EGFR.

FIG. 15. Mitogenic response to EGF of BaF/3 cells expressing wt ormutant EGFR. [³H]Thymidine incorporation in cells treated with controlbuffer (open circles) or increasing concentrations of EGF (filledcircles) was determined as described in Experimental procedures.

FIG. 16. Comparison of mAb528 and mAb806 antibody binding to BaF/3 cellsexpressing EGFR lacking the CR1-loop. Cells expressing the wt, Δ2-7 orΔ-CR1-loop EGFRs were stained with either mAb528 (dark line) or mAb806(filled grey) as described in FIG. 2, and analysed on a FACScan. Themedian fluorescence channel for each peak was determined using thestatistical analysis software in CellQuest and used to calculate theratios between the two antibodies. Control fluorescence of anirrelevant, class-matched antibody is presented as a dotted lineoverlay.

FIG. 17A-17E. EGFR conformations and activation. The EGFR undergoes amajor conformational change during the transition from the low affinityto the high affinity state. The low affinity conformation (A) istethered by intra-molecular interactions between the two cysteines-richdomains CR1 and CR2. The tethered monomer (A) is in equilibrium witheither the tethered dimer (B) or a high affinity untethered monomer (F).It appears that transmembrane (TM) and/or kinase domains drive theformation of both the tethered dimmer (B) and the untethered dimer (C).The tethered dimer (B) is depicted in the cartoon with inter-molecularcontacts between the both the ECD and kinase domains. The tethered formsof the receptor are low affinity. The untethered monomer and dimer havehigher affinity. The intracellular kinase domains of the untethereddimer are not activated until ligand (eg EGF or TGF-α) binding induces afurther reorientation in the dimer-ligand complex (D). Thereceptor-ligand complex is capable of forming higher order oligomers (egtetramers, E). The ligand binding affinity is further modulated byinside-out signaling (eg ATP). Although ligand binding anddimerization/oligomerization lead to kinase activation and substratephosphorylation, signaling from the receptor is also regulated byinternalization, degradation and de-phosphorylation.

FIG. 18A-18D depict flow cytometry data for mAb 806 binding to yeastsurface displayed EGFR fragment 273-621. EGFR display fluorescence asdetected by the c-myc tag is shown on the abscissa, and mAb 806 bindingis shown on the ordinate. (A) Sort 1 (10 nM mAb 806) and sort 2 (75 nM),with sort gates indicated by solid lines. (B-D) Representative mutantsof (B), +(C), and ++(D) binding, and positive and negative controls at75 nM. WT=wild-type EGFR 273-621.

FIG. 19 depicts titration of mAb 806 against yeast surface displayedEGFR 273-621 and mutants. Black, wild-type (++); dark gray, C287R (+);light gray, E293K (−). A global fit to a single site binding model wasperformed with three independent sets of data (Squares, triangles, anddiamonds represent separate sets).

FIG. 20A-20D. mAb 806 epitope. (A-B) Front and back views of the epitopein chain a of the EGFR-EGF dimer structure (PDB ID 1IVO). The dimerstructure is used because Glu293 is not resolved in the monomerstructure (PDB ID 1NQL). Residues shown in color are mutants isolatedfrom the library for loss of binding. Red, residues that also cause lossof binding upon alanine substitution; orange, residues that do not;gray, residues that were not isolated from the library and exhibited noloss of binding upon alanine substitution. (C) The epitope isconstrained by a disulfide bond and two salt bridges (Glu293-Arg300 andAsp297-Lys301). Negatively charged residues, red; positive, blue;cysteines, yellow. Image includes residues 287-302 on both EGFRmolecules in dimer structure (PDB ID 1IVO). (D) mAb 806 epitope inautoinhibited EGFR monomer, colored as in (A), with the rest of EGFRblue.

DETAILED DESCRIPTION

In accordance with the present invention there may be employedconventional molecular biology, microbiology, and recombinant DNAtechniques within the skill of the art. Such techniques are explainedfully in the literature. See, e.g., Sambrook et al, “Molecular Cloning:A Laboratory Manual” (1989); “Current Protocols in Molecular Biology”Volumes I-III [Ausubel, R. M., ed. (1994)]; “Cell Biology: A LaboratoryHandbook” Volumes I-III [J. E. Celis, ed. (1994))]; “Current Protocolsin Immunology” Volumes I-III [Coligan, J. E., ed. (1994)];“Oligonucleotide Synthesis” (M. J. Gait ed. 1984); “Nucleic AcidHybridization” [B. D. Hames & S. J. Higgins eds. (1985)]; “TranscriptionAnd Translation” [B. D. Hames & S. J. Higgins, eds. (1984)]; “AnimalCell Culture” [R. I. Freshney, ed. (1986)]; “Immobilized Cells AndEnzymes” [IRL Press, (1986)]; B. Perbal, “A Practical Guide To MolecularCloning” (1984).

Therefore, if appearing herein, the following terms shall have thedefinitions set out below.

The terms “growth factor receptor peptides, “receptor epitope peptides”,“EGF family receptor peptides”, “EGF receptor peptides”, “EGFRepitopes”, “EGFR peptides” and any variants not specifically listed, maybe used herein interchangeably, and as used throughout the presentapplication and claims refer to peptide material including single ormultiple peptides, and extends to those peptides having the amino acidsequence data described herein and presented in any of SEQ ID NOS: 1-14and in TABLES 1 and 2, and variants thereof, and the profile ofactivities set forth herein and in the Claims. Accordingly, proteinsdisplaying substantially equivalent or altered activity are likewisecontemplated. These modifications may be deliberate, for example, suchas modifications obtained through site-directed mutagenesis, or may beaccidental, such as those obtained through mutations in hosts that areproducers of the complex or its named subunits. Methods for generatingand testing modifications of the receptor epitope peptides, includingvariants thereof, including but not limited to, by site-directedmutagenesis or random mutagenesis are well known to those skilled in theart, and include those described and exemplified herein and as providedin Example 3 hereof. Also, the terms “growth factor receptor peptides,“receptor epitope peptides”, “EGF family receptor peptides”, “EGFreceptor peptides”, “EGFR epitopes”, “EGFR peptides” are intended toinclude within their scope proteins and peptides specifically recitedherein as well as all substantially homologous analogs and allelicvariations.

The amino acid residues described herein are preferred to be in the “L”isomeric form. However, residues in the “D” isomeric form can besubstituted for any L-amino acid residue, as long as the desiredfunctional property of immunoglobulin-binding is retained by thepolypeptide. NH₂ refers to the free amino group present at the aminoterminus of a polypeptide. COOH refers to the free carboxy group presentat the carboxy terminus of a polypeptide. In keeping with standardpolypeptide nomenclature, J. Biol. Chem., 243:3552-59 (1969),abbreviations for amino acid residues are shown in the following Tableof Correspondence:

TABLE OF CORRESPONDENCE SYMBOL 1-Letter 3-Letter AMINO ACID Y Tyrtyrosine G Gly glycine F Phe phenylalanine M Met methionine A Alaalanine S Ser serine I Ile isoleucine L Leu leucine T Thr threonine VVal valine P Pro proline K Lys lysine H His histidine Q Gln glutamine EGlu glutamic acid W Trp tryptophan R Arg arginine D Asp aspartic acid NAsn asparagine C Cys cysteine

It should be noted that all amino-acid residue sequences are representedherein by formulae whose left and right orientation is in theconventional direction of amino-terminus to carboxy-terminus.Furthermore, it should be noted that a dash at the beginning or end ofan amino acid residue sequence indicates a peptide bond to a furthersequence of one or more amino-acid residues. The above Table ispresented to correlate the three-letter and one-letter notations whichmay appear alternately herein.

A “replicon” is any genetic element (e.g., plasmid, chromosome, virus)that functions as an autonomous unit of DNA replication in vivo; i.e.,capable of replication under its own control.

A “vector” is a replicon, such as plasmid, phage or cosmid, to whichanother DNA segment may be attached so as to bring about the replicationof the attached segment.

A “DNA molecule” refers to the polymeric form of deoxyribonucleotides(adenine, guanine, thymine, or cytosine) in its either single strandedform, or a double-stranded helix. This term refers only to the primaryand secondary structure of the molecule, and does not limit it to anyparticular tertiary forms. Thus, this term includes double-stranded DNAfound, inter alia, in linear DNA molecules (e.g., restrictionfragments), viruses, plasmids, and chromosomes. In discussing thestructure of particular double-stranded DNA molecules, sequences may bedescribed herein according to the normal convention of giving only thesequence in the 5′ to 3′ direction along the nontranscribed strand ofDNA (i.e., the strand having a sequence homologous to the mRNA).

An “origin of replication” refers to those DNA sequences thatparticipate in DNA synthesis.

A DNA “coding sequence” is a double-stranded DNA sequence which istranscribed and translated into a polypeptide in vivo when placed underthe control of appropriate regulatory sequences. The boundaries of thecoding sequence are determined by a start codon at the 5′ (amino)terminus and a translation stop codon at the 3′ (carboxyl) terminus. Acoding sequence can include, but is not limited to, prokaryoticsequences, cDNA from eukaryotic mRNA, genomic DNA sequences fromeukaryotic (e.g., mammalian) DNA, and even synthetic DNA sequences. Apolyadenylation signal and transcription termination sequence willusually be located 3′ to the coding sequence.

Transcriptional and translational control sequences are DNA regulatorysequences, such as promoters, enhancers, polyadenylation signals,terminators, and the like, that provide for the expression of a codingsequence in a host cell.

A “promoter sequence” is a DNA regulatory region capable of binding RNApolymerase in a cell and initiating transcription of a downstream (3′direction) coding sequence. For purposes of defining the presentinvention, the promoter sequence is bounded at its 3′ terminus by thetranscription initiation site and extends upstream (5′ direction) toinclude the minimum number of bases or elements necessary to initiatetranscription at levels detectable above background. Within the promotersequence will be found a transcription initiation site (convenientlydefined by mapping with nuclease S1), as well as protein binding domains(consensus sequences) responsible for the binding of RNA polymerase.Eukaryotic promoters will often, but not always, contain “TATA” boxesand “CAT” boxes. Prokaryotic promoters contain Shine-Dalgarno sequencesin addition to the −10 and −35 consensus sequences.

An “expression control sequence” is a DNA sequence that controls andregulates the transcription and translation of another DNA sequence. Acoding sequence is “under the control” of transcriptional andtranslational control sequences in a cell when RNA polymerasetranscribes the coding sequence into mRNA, which is then translated intothe protein encoded by the coding sequence.

A “signal sequence” can be included before the coding sequence. Thissequence encodes a signal peptide, N-terminal to the polypeptide, thatcommunicates to the host cell to direct the polypeptide to the cellsurface or secrete the polypeptide into the media, and this signalpeptide is clipped off by the host cell before the protein leaves thecell. Signal sequences can be found associated with a variety ofproteins native to prokaryotes and eukaryotes.

The term “oligonucleotide,” as used herein in referring to the probe ofthe present invention, is defined as a molecule comprised of two or moreribonucleotides, preferably more than three. Its exact size will dependupon many factors which, in turn, depend upon the ultimate function anduse of the oligonucleotide.

The term “primer” as used herein refers to an oligonucleotide, whetheroccurring naturally as in a purified restriction digest or producedsynthetically, which is capable of acting as a point of initiation ofsynthesis when placed under conditions in which synthesis of a primerextension product, which is complementary to a nucleic acid strand, isinduced, i.e., in the presence of nucleotides and an inducing agent suchas a DNA polymerase and at a suitable temperature and pH. The primer maybe either single-stranded or double-stranded and must be sufficientlylong to prime the synthesis of the desired extension product in thepresence of the inducing agent. The exact length of the primer willdepend upon many factors, including temperature, source of primer anduse of the method. For example, for diagnostic applications, dependingon the complexity of the target sequence, the oligonucleotide primertypically contains 15-25 or more nucleotides, although it may containfewer nucleotides.

The primers herein are selected to be “substantially” complementary todifferent strands of a particular target DNA sequence. This means thatthe primers must be sufficiently complementary to hybridize with theirrespective strands. Therefore, the primer sequence need not reflect theexact sequence of the template. For example, a non-complementarynucleotide fragment may be attached to the 5′ end of the primer, withthe remainder of the primer sequence being complementary to the strand.Alternatively, non-complementary bases or longer sequences can beinterspersed into the primer, provided that the primer sequence hassufficient complementarity with the sequence of the strand to hybridizetherewith and thereby form the template for the synthesis of theextension product.

As used herein, the terms “restriction endonucleases” and “restrictionenzymes” refer to bacterial enzymes, each of which cut double-strandedDNA at or near a specific nucleotide sequence.

A cell has been “transformed” by exogenous or heterologous DNA when suchDNA has been introduced inside the cell. The transforming DNA may or maynot be integrated (covalently linked) into chromosomal DNA making up thegenome of the cell. In prokaryotes, yeast, and mammalian cells forexample, the transforming DNA may be maintained on an episomal elementsuch as a plasmid. With respect to eukaryotic cells, a stablytransformed cell is one in which the transforming DNA has becomeintegrated into a chromosome so that it is inherited by daughter cellsthrough chromosome replication. This stability is demonstrated by theability of the eukaryotic cell to establish cell lines or clonescomprised of a population of daughter cells containing the transformingDNA. A “clone” is a population of cells derived from a single cell orcommon ancestor by mitosis. A “cell line” is a clone of a primary cellthat is capable of stable growth in vitro for many generations.

Two DNA sequences are “substantially homologous” when at least about 75%(preferably at least about 80%, and most preferably at least about 90 or95%) of the nucleotides match over the defined length of the DNAsequences. Sequences that are substantially homologous can be identifiedby comparing the sequences using standard software available in sequencedata banks, or in a Southern hybridization experiment under, forexample, stringent conditions as defined for that particular system.Defining appropriate hybridization conditions is within the skill of theart. See, e.g., Maniatis et al., supra; DNA Cloning, Vols. I & II,supra; Nucleic Acid Hybridization, supra.

It should be appreciated that also within the scope of the presentinvention are DNA sequences encoding the receptor peptides of thepresent invention which code for a polypeptide having the same aminoacid sequence as any of SEQ ID NOS: 1-14, and which may be degenerate toone another. By “degenerate to” is meant that a different three-lettercodon is used to specify a particular amino acid. It is well known inthe art that the following codons can be used interchangeably to codefor each specific amino acid:

Phenylalanine (Phe or F) UUU or UUC Leucine (Leu or L) UUA or UUG or CUUor CUC or CUA or CUG Isoleucine (Ile or I) AUU or AUC or AUA Methionine(Met or M) AUG Valine (Val or V) GUU or GUC of GUA or GUG Serine (Ser orS) UCU or UCC or UCA or UCG or AGU or AGC Proline (Pro or P) CCU or CCCor CCA or CCG Threonine (Thr or T) ACU or ACC or ACA or ACG Alanine (Alaor A) GCU or GCG or GCA or GCG Tyrosine (Tyr or Y) UAU or UAC Histidine(His or H) CAU or CAC Glutamine (Gln or Q) CAA or CAG Asparagine (Asn orN) AAU or AAC Lysine (Lys or K) AAA or AAG Aspartic Acid (Asp or D) GAUor GAC Glutamic Acid (Glu or E) GAA or GAG Cysteine (Cys or C) UGU orUGC Arginine (Arg or R) CGU or CGC or CGA or CGG or AGA or AGG Glycine(Gly or G) GGU or GGC or GGA or GGG Tryptophan (Trp or W) UGGTermination codon UAA (ochre) or UAG (amber) or UGA (opal)

It should be understood that the codons specified above are for RNAsequences. The corresponding codons for DNA have a T substituted for U.

Mutations can be made in DNA sequences encoding any of SEQ ID NOS: 1-14such that a particular codon is changed to a codon which codes for adifferent amino acid. Such a mutation is generally made by making thefewest nucleotide changes possible. A substitution mutation of this sortcan be made to change an amino acid in the resulting protein in anon-conservative manner (i.e., by changing the codon from an amino acidbelonging to a grouping of amino acids having a particular size orcharacteristic to an amino acid belonging to another grouping) or in aconservative manner (i.e., by changing the codon from an amino acidbelonging to a grouping of amino acids having a particular size orcharacteristic to an amino acid belonging to the same grouping). Such aconservative change generally leads to less change in the structure andfunction of the resulting protein. A non-conservative change is morelikely to alter the structure, activity or function of the resultingprotein. The present invention should be considered to include sequencescontaining conservative changes which do not significantly alter theactivity or binding characteristics of the resulting protein.

The following is one example of various groupings of amino acids:

Amino acids with nonpolar R groups

Alanine, Valine, Leucine, Isoleucine, Proline, Phenylalanine,Tryptophan, Methionine

Amino acids with uncharged polar R groups

Glycine, Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine

Amino acids with charged polar R groups (negatively charged at Ph 6.0)

Aspartic acid, Glutamic acid

Basic amino acids (positively charged at pH 6.0)

Lysine, Arginine, Histidine (at pH 6.0)

Another grouping may be those amino acids with phenyl groups:

Phenylalanine, Tryptophan, Tyrosine

Another grouping may be according to molecular weight (i.e., size of Rgroups):

Glycine 75 Alanine 89 Serine 105 Proline 115 Valine 117 Threonine 119Cysteine 121 Leucine 131 Isoleucine 131 Asparagine 132 Aspartic acid 133Glutamine 146 Lysine 146 Glutamic acid 147 Methionine 149 Histidine (atpH 6.0) 155 Phenylalanine 165 Arginine 174 Tyrosine 181 Tryptophan 204

Particularly preferred substitutions are:

Lys for Arg and vice versa such that a positive charge may bemaintained;

Glu for Asp and vice versa such that a negative charge may bemaintained;

Ser for Thr such that a free —OH can be maintained; and

Gln for Asn such that a free NH₂ can be maintained.

Amino acid substitutions may also be introduced to substitute an aminoacid with a particularly preferable property. For example, a Cys may beintroduced a potential site for disulfide bridges with another Cys. AHis may be introduced as a particularly “catalytic” site (i.e., His canact as an acid or base and is the most common amino acid in biochemicalcatalysis). Pro may be introduced because of its particularly planarstructure, which induces—turns in the protein's structure.

Two amino acid sequences are “substantially homologous” when at leastabout 70% of the amino acid residues (preferably at least about 80%, andmost preferably at least about 90 or 95%) are identical, or representconservative substitutions.

A “heterologous” region of the DNA construct is an identifiable segmentof DNA within a larger DNA molecule that is not found in associationwith the larger molecule in nature. Thus, when the heterologous regionencodes a mammalian gene, the gene will usually be flanked by DNA thatdoes not flank the mammalian genomic DNA in the genome of the sourceorganism. Another example of a heterologous coding sequence is aconstruct where the coding sequence itself is not found in nature (e.g.,a cDNA where the genomic coding sequence contains introns, or syntheticsequences having codons different than the native gene). Allelicvariations or naturally-occurring mutational events do not give rise toa heterologous region of DNA as defined herein.

A DNA sequence is “operatively linked” to an expression control sequencewhen the expression control sequence controls and regulates thetranscription and translation of that DNA sequence. The term“operatively linked” includes having an appropriate start signal (e.g.,ATG) in front of the DNA sequence to be expressed and maintaining thecorrect reading frame to permit expression of the DNA sequence under thecontrol of the expression control sequence and production of the desiredproduct encoded by the DNA sequence. If a gene that one desires toinsert into a recombinant DNA molecule does not contain an appropriatestart signal, such a start signal can be inserted in front of the gene.

The term “standard hybridization conditions” refers to salt andtemperature conditions substantially equivalent to 5×SSC and 65° C. forboth hybridization and wash. However, one skilled in the art willappreciate that such “standard hybridization conditions” are dependenton particular conditions including the concentration of sodium andmagnesium in the buffer, nucleotide sequence length and concentration,percent mismatch, percent formamide, and the like. Also important in thedetermination of “standard hybridization conditions” is whether the twosequences hybridizing are RNA-RNA, DNA-DNA or RNA-DNA. Such standardhybridization conditions are easily determined by one skilled in the artaccording to well known formulae, wherein hybridization is typically10-20° C. below the predicted or determined T_(m) with washes of higherstringency, if desired.

An “antibody” is any immunoglobulin, including antibodies and fragmentsthereof, that binds a specific epitope. The term encompasses polyclonal,monoclonal, and chimeric antibodies, the last mentioned described infurther detail in U.S. Pat. Nos. 4,816,397 and 4,816,567.

As antibodies can be modified in a number of ways, the term “antibody”should be construed as covering any specific molecule or substancehaving a binding domain with the required specificity. Thus, this termcovers antibody fragments, derivatives, functional equivalents andhomologues of antibodies, including any polypeptide comprising animmunoglobulin binding domain, whether natural or wholly or partiallysynthetic. Chimeric molecules comprising an immunoglobulin bindingdomain, or equivalent, fused to another polypeptide are thereforeincluded. Cloning and expression of chimeric antibodies are described inEP-A-0120694 and EP-A-0125023 and U.S. Pat. Nos. 4,816,397 and4,816,567.

It has been shown that fragments of a whole antibody can perform thefunction of binding antigens. Examples of binding fragments are (i) theFab fragment consisting of VL, VH, CL and CH1 domains; (ii) the Fdfragment consisting of the VH and CH1 domains; (iii) the Fv fragmentconsisting of the VL and VH domains of a single antibody; (iv) the dAbfragment (Ward, E. S. et al., Nature 341, 544-546 (1989)) which consistsof a VH domain; (v) isolated CDR regions; (vi) F(ab′)2 fragments, abivalent fragment comprising two linked Fab fragments (vii) single chainFv molecules (scFv), wherein a VH domain and a VL domain are linked by apeptide linker which allows the two domains to associate to form anantigen binding site (Bird et al, Science, 242, 423-426, 1988; Huston etal, PNAS USA, 85, 5879-5883, 1988); (viii) multivalent antibodyfragments (scFv dimers, trimers and/or tetramers (Power and Hudson, JImmunol. Methods 242: 193-204 9 (2000)) (ix) bispecific single chain Fvdimers (PCT/US92/09965) and (x) “diabodies”, multivalent ormultispecific fragments constructed by gene fusion (WO94/13804; P.Holliger et al Proc. Natl. Acad. Sci. USA 90 6444-6448, (1993)).

An “antibody combining site” is that structural portion of an antibodymolecule comprised of heavy and light chain variable and hypervariableregions that specifically binds antigen.

The phrase “antibody molecule” in its various grammatical forms as usedherein contemplates both an intact immunoglobulin molecule and animmunologically active portion of an immunoglobulin molecule.

Exemplary antibody molecules are intact immunoglobulin molecules,substantially intact immunoglobulin molecules and those portions of animmunoglobulin molecule that contains the paratope, including thoseportions known in the art as Fab, Fab′, F(ab′)₂ and F(v), which portionsare preferred for use in the therapeutic methods described herein.

Fab and F(ab′)₂ portions of antibody molecules are prepared by theproteolytic reaction of papain and pepsin, respectively, onsubstantially intact antibody molecules by methods that are well-known.See for example, U.S. Pat. No. 4,342,566 to Theofilopolous et al. Fab′antibody molecule portions are also well-known and are produced fromF(ab′)₂ portions followed by reduction of the disulfide bonds linkingthe two heavy chain portions as with mercaptoethanol, and followed byalkylation of the resulting protein mercaptan with a reagent such asiodoacetamide. An antibody containing intact antibody molecules ispreferred herein.

The phrase “monoclonal antibody” in its various grammatical forms refersto an antibody having only one species of antibody combining sitecapable of immunoreacting with a particular antigen. A monoclonalantibody thus typically displays a single binding affinity for anyantigen with which it immunoreacts. A monoclonal antibody may thereforecontain an antibody molecule having a plurality of antibody combiningsites, each immunospecific for a different antigen; e.g., a bispecific(chimeric) monoclonal antibody.

The phrase “pharmaceutically acceptable” refers to molecular entitiesand compositions that are physiologically tolerable and do not typicallyproduce an allergic or similar untoward reaction, such as gastric upset,dizziness and the like, when administered to a human.

The phrase “therapeutically effective amount” is used herein to mean anamount sufficient to prevent, and preferably reduce by at least about 30percent, more preferably by at least 50 percent, most preferably by atleast 90 percent, a clinically significant change size or in the S phaseactivity of a target cellular mass, or other feature of pathology suchas for example antibody response, T cell or B cell response, reductionin EGFR expression.

The term “adjuvant” refers to a compound or mixture that enhances theimmune response, particularly to an antigen. An adjuvant can serve as atissue depot that slowly releases the antigen and also as a lymphoidsystem activator that non-specifically enhances the immune response(Hood et al., Immunology, Second Ed., 1984, Benjamin/Cummings: MenloPark, Calif., p. 384). Often, a primary challenge with an antigen alone,in the absence of an adjuvant, will fail to elicit a humoral or cellularimmune response. Previously known and utilized adjuvants include, butare not limited to, complete Freund's adjuvant, incomplete Freund'sadjuvant, saponin, mineral gels such as aluminum hydroxide, surfaceactive substances such as lysolecithin, pluronic polyols, polyanions,peptides, oil or hydrocarbon emulsions, keyhole limpet hemocyanins,dinitrophenol, and potentially useful human adjuvant such as BCG(bacille Calmette-Guerin) and Corynebacterium parvum. Mineral saltadjuvants include but are not limited to: aluminum hydroxide, aluminumphosphate, calcium phosphate, zinc hydroxide and calcium hydroxide.Preferably, the adjuvant composition further comprises a lipid of fatemulsion comprising about 10% (by weight) vegetable oil and about 1-2%(by weight) phospholipids. Preferably, the adjuvant composition furtheroptionally comprises an emulsion form having oily particles dispersed ina continuous aqueous phase, having an emulsion forming polyol in anamount of from about 0.2% (by weight) to about 49% (by weight),optionally a metabolizable oil in an emulsion-forming amount of up to15% (by weight), and optionally a glycol ether-based surfactant in anemulsion-stabilizing amount of up to about 5% (by weight). Otherexamples of adjuvants include monophosphoryl lipid A (MPL, SmithKlineBeecham), a congener obtained after purification and acid hydrolysis ofSalmonella Minnesota Re 595 lipopolysaccharide; saponins including QS21(SmithKline Beecham), a pure QA-21 saponin purified from Quilljasaponaria extract; DQS21, described in PCT application WO96/33739(SmithKline Beecham); ISCOM (CSL Ltd., Parkville, Victoria, Australia)derived from the bark of the Quillaia saponaria molina tree; QS-7,QS-17, QS-18, and QS-L1 (So et al., Mol. Cells 7:178-186, 1997);montanide; alum; CpG oligonucleotides (see e.g. Kreig et al., Nature374:546-9, 1995); various water-in-oil emulsions prepared frombiodegradable oils such as squalene and/or tocopherol; and factors thatare taken up by the so-called ‘toll-like receptor 7’ on certain immunecells that are found in the outside part of the skin, such as imiquimod(3M, St. Paul, Minn.). Particularly, the antigens may be administeredmixed with a combination of DQS21/MPL. The ratio of DQS21 to MPLtypically will be about 1:10 to 10:1, preferably about 1:5 to 5:1 andmore preferably about 1:1. Typically for human administration, DQS21 andMPL will be present in a vaccine formulation in the range of about 1 μgto about 100 μg. Other adjuvants are known in the art and can be used inthe invention (see, e.g. Goding, Monoclonal Antibodies: Principles andPractice, 2nd Ed., 1986). Methods for the preparation of mixtures oremulsions of polypeptide and adjuvant are well known to those of skillin the art of inducing and/or enhancing an immune response and the artof vaccination.

As used herein, the term “immunomodulator” refers to an agent which isable to modulate an immune response or immunological response. Suchmodulation includes the enhancement of antibody production, of humoralresponse, of cellular immune response. Examples of immunomodulatorsinclude, but are not limited to, adjuvants, cytokines, interleukins,chemokines and growth factors.

The term “effective amount” of an immunomodulator refers to an amount ofan immunomodulator sufficient to enhance a vaccine-induced immuneresponse, be it cell-mediated, humoral or antibody-mediated. Aneffective amount of an immunomodulator, if injected, can be in the rangeof about 0.1-1,000 μg, preferably 1-900 μg, more preferably 5-500 μg,for a human subject, or in the range of about 0.01-10.0 μg/Kg bodyweight of the subject animal. This amount may vary to some degreedepending on the mode of administration, but will be in the same generalrange. If more than one immunomodulator is used, each one may be presentin these amounts or the total amount may fall within this range. Aneffective amount of an antigen may be an amount capable of eliciting ademonstrable immune response in the absence of an immunomodulator. Theappropriate amount of antigen to be used is dependent on the specificantigen and is well known in the art.

The exact effective amount necessary will vary from subject to subject,depending on the species, age and general condition of the subject, theseverity of the condition being treated, the mode of administration,etc. Thus, it is not possible to specify an exact effective amount.However, the appropriate effective amount may be determined by one ofordinary skill in the art using only routine experimentation or priorknowledge in the vaccine art.

An “immunological response” to a composition or vaccine comprised of anantigen is the development in the host of a cellular- and/orantibody-mediated immune response to the composition or vaccine ofinterest. Usually, such a response consists of the subject producingantibodies, B cells, helper T cells, suppressor T cells, and/orcytotoxic T cells directed specifically to an antigen or antigensincluded in the composition or vaccine of interest.

As used herein, “pg” means picogram, “ng” means nanogram, “ug” or “μg”mean microgram, “mg” means milligram, “ul” or “μl” mean microliter, “ml”means milliliter, “l” means liter.

The term “aberrant expression” in its various grammatical forms may meanand include any heightened or altered expression or overexpression of aprotein in a tissue, e.g. an increase in the amount of a protein, causedby any means including enhanced expression or translation, modulation ofthe promoter or a regulator of the protein, amplification of a gene fora protein, or enhanced half-life or stability, such that more of theprotein exists or can be detected at any one time, in contrast to anon-overexpressed state. Aberrant expression includes and contemplatesany scenario or alteration wherein the protein expression orpost-translational modification machinery in a cell is taxed orotherwise disrupted due to enhanced expression or increased levels oramounts of a protein, including wherein an altered protein, as inmutated protein or variant due to sequence alteration, deletion orinsertion, or altered folding is expressed.

It is important to appreciate that the term “aberrant expression” hasbeen specifically chosen herein to encompass the state where abnormal(usually increased) quantities/levels of the protein are present,irrespective of the efficient cause of that abnormal quantity or level.Thus, abnormal quantities of protein may result from overexpression ofthe protein in the absence of gene amplification, which is the case e.g.in many cellular/tissue samples taken from the head and neck of subjectswith cancer, while other samples exhibit abnormal protein levelsattributable to gene amplification.

In this latter connection, certain of the work of the inventors that ispresented herein to illustrate the invention includes the analysis ofsamples certain of which exhibit abnormal protein levels resulting fromamplification of a growth factor receptor, including an EGF familyreceptor, particularly including EGFR. This therefore accounts for thepresentation herein of experimental findings where reference is made toamplification and for the use of the terms “amplification/amplified” andthe like in describing abnormal levels of growth factor receptor, EGFfamily receptor, EGFR. However, it is the observation of abnormalquantities or levels of the protein that defines the environment orcircumstance where clinical intervention as by resort to the bindingmembers of the invention is contemplated, and for this reason, thepresent specification considers that the term “aberrant expression” morebroadly captures the causal environment that yields the correspondingabnormality in growth factor receptor, EGF family receptor, EFGR levels.

Accordingly, while the terms “overexpression” and “amplification” intheir various grammatical forms are understood to have distincttechnical meanings, they are to be considered equivalent to each other,insofar as they represent the state where abnormal growth factorreceptor, EGF family receptor, EFGR protein levels are present in thecontext of the present invention. Consequently, the term “aberrantexpression” has been chosen as it is believed to subsume the terms“overexpression” and “amplification” within its scope for the purposesherein, so that all terms may be considered equivalent to each other asused herein.

The present invention relates to receptor epitopes, particularly growthfactor receptor epitopes, which can be utilized in generating antibodieswhich have anti-tumor capacity and activity or stimulating animmunological response which is an anti-tumor reponse. The growth factorreceptor epitopes include loop epitopes that are exposed in transitionalforms of the growth factor receptor and are capable of generatingantibodies which recognize transitional forms of the receptor, therebymodulating, including preventing or inhibiting, their activation,including the change from an inactive to active ligand-boundconformation. The invention provides receptor epitopes, particularly EGFfamily receptor epitopes, most particularly EGFR epitopes, which can beutilized in generating antibodies which have anti-tumor capacity andactivity or stimulating an immunological response which is an anti-tumorresponse. In a general aspect the invention provides a receptor epitope,particularly an EGF receptor epitope or EGF receptor family epitope,which is found in tumorigenic, hyperproliferative or abnormal cells andis not detectable or transitional in normal or wild type cells.

The present invention describes the existence and exposure of an epitopepeptide, particularly a loop peptide, which is bound at each N-terminaland C-terminal end by a cysteine, forming a disulfide loop peptide, in agrowth factor receptor, particularly the EGFR. This loop peptide isexposed in an untethered, transitional conformation, and its presence oramount is altered or increased in instances including autocrine ligandproduction (ligand drives the EGFR towards active dimers),ligand-independent receptor activation (an event largely restricted tocells that over-express the receptor), alterations in glycosylation thatalter the level of untethering or a combination of any of thesepossibilities.

Although the sequence homology of the EGFR mAb806 loop 287-302 epitope(CGADSYEMEEDGVRKC (SEQ ID NO: 1)) is relatively low in EGF familymembers ErbB3 and ErbB4, the size and location of the cysteine loop isconserved. Furthermore, there are two amino acid residues completelyconserved (E293 and G298) and a further two where charge is conserved(E295 and R300). Finally, the overall structure of ErbB3 (and probablyErbB4), is very similar to that of the EGFR in that it adopts a tetheredconformation that presumably untethers during activation (Cho, H. S. andLeahy, D. J. (2002) Science 297:1330-1333). Thus, antibodies targeted tothe equivalent cysteine loop in ErbB3/B4 are provided herein as usefulin having similar properties to mAb 806 (i.e. specificity restricted totumors and the ability to block receptor activation). More broadly, thegeneration of antibodies to transitional forms of growth factorreceptors represents a novel way of reducing normal tissue targeting yetretaining anti-signaling activity.

TABLE 1 below provides a comparison of the loop sequence of EGF familymembers EGFR, ErbB2, ErbB3 and ErbB4.

TABLE 1

In addition, a Genbank BLAST search utilizing the EGFR mAb806 loop287-302 epitope (CGADSYEMEEDGVRKC (SEQ ID NO: 1)) identifies naturalalleles and variants of this loop epitope peptide sequence in variousmammalian EGFRs (TABLE 2).

TABLE 2 EGF peptide C G A D S Y E M E E D G V R K C Mouse EGFR etc. gi1352359 P Y V I gi 458123 and gi 12836452 Chick EGFR gi 119223 N T T V NRabbit gi 13173350 P V gi 13173351 Pig gi 21913175 S S V gi 21913176 EGFgi 224020 A

In accordance with the present invention, growth factor receptorpeptides, particularly EGFR peptides are provided which are capable ofgenerating antibodies, particularly monoclonal antibodies, which haveanti-tumor activity.

In accordance with the present invention, growth factor receptorpeptides, particularly EGFR peptides are provided which are capable ofgenerating antibodies which are capable of recognizing EGFR which isfound in tumorigenic, hyperproliferative or abnormal cells and is notdetectable or transitional in normal or wild type cells.

The growth factor receptor peptides, particularly the EGF familyreceptor peptides, of the present invention provide diagnostic andtherapeutic uses to identify, characterize and target a number of tumortypes, for example, head and neck, breast, lung, bladder, colon orprostate tumors and glioma, without the problems associated with normaltissue uptake that may be seen with previously known growth factorreceptor, including EGFR, antibodies.

The present invention encompasses isolated polypeptides comprising anamino acid sequence of a growth factor receptor peptide having an aminoacid sequence selected from any of SEQ ID NOS: 1-14. The presentinvention further encompasses variants or mutants of any of SEQ ID NOS:1-14, wherein one or more amino acid is substituted, including by aconservative or non-conservative amino acid. Any such variant or mutantpeptide which is capable of being recognized or bound by the mAb 806antibody, or a recombinant or synthetic antibody derived therefrom, orwhich is capable of generating antibody(ies) having a characteristic ofmAb806 is encompassed by the present invention. In particular, any suchpeptide(s) may be capable of generating antibodies which recognizegrowth factor receptor and have anti-tumor activity. The isolatedpeptides, including combinations of one or more thereof, are suitablefor use in generating antibodies which recognize growth factor receptorand have anti-tumor activity and in immunizing animals, particularlymammals, most particularly humans, who have cancer or tumor disease.

As stated above, the present invention also relates to a recombinant DNAmolecule or cloned gene, or a degenerate variant thereof, which encodesgrowth factor receptor epitope, or an immunogenic fragment thereof, thathas an amino acid sequence set forth in any of SEQ ID NOS: 1-14;preferably a nucleic acid molecule, in particular a recombinant DNAmolecule or cloned gene, encoding EGF family receptor epitope selectedfrom any of SEQ ID NOS: 1-14.

As discussed earlier, the EGF family receptor epitopes or immunogenicfragments thereof, particularly selected from an EGF receptor epitope ofany of SEQ ID NOS: 1-14, may be prepared in pharmaceutical compositions,with a suitable carrier and at a strength effective for administrationby various means to a patient having a tumor or cancer for the treatmentthereof. A variety of administrative techniques may be utilized, amongthem parenteral techniques such as subcutaneous, intravenous andintraperitoneal injections, catheterizations and the like. Averagequantities of the peptide(s) or immunogenic fragments thereof may varyand in particular should be based upon the recommendations andprescription of a qualified physician or veterinarian.

Antibodies

In a still further aspect, the present invention provides a purifiedantibody to an EGF family receptor peptide selected from any of SEQ IDNOS: 1-14.

Antibodies against the isolated polypeptides of the present inventioninclude naturally raised and recombinantly prepared antibodies. Thesemay include both polyclonal and monoclonal antibodies prepared by knowngenetic techniques, as well as bi-specific antibodies, and antibodiesincluding other functionalities suiting them for diagnostic use. Suchantibodies can be used therapeutically to treat patients with tumorshaving an abbereant expression of the EGFR or any of its family members,including but not limited to head and neck cancer, breast cancer, lungcancer, ovarian cancer, bladder cancer, laryngeal cancer, squamous cellcarcinoma, or prostate tumors and glioma. Such antibodies can also beused immunoassays to characterize tumors or diagnose cancer includinghead and neck cancer, breast cancer, lung cancer, ovarian cancer,bladder cancer, laryngeal cancer, squamous cell carcinoma, or prostatetumors and glioma. The antibodies can also be used for passiveimmunization to reduce tumors or treat cancer including from head andneck cancer, breast cancer, lung cancer, ovarian cancer, bladder cancer,laryngeal cancer, squamous cell carcinoma, or prostate tumors andglioma.

Also, antibodies including both polyclonal and monoclonal antibodies,and drugs that modulate the exposure or activity of the receptor epitopepeptides and/or their subunits may possess certain diagnosticapplications and may for example, be utilized for the purpose ofdetecting and/or measuring conditions such as viral infection or thelike. For example, the receptor peptides or immunogenic fragmentsthereof may be used to produce both polyclonal and monoclonal antibodiesin a variety of cellular media, by known techniques such as thehybridoma technique utilizing, for example, fused mouse spleenlymphocytes and myeloma cells. Likewise, small molecules that mimic orantagonize the activity(ies) of the receptor peptides or epitope loopsof the invention may be discovered or synthesized, and may be used indiagnostic and/or therapeutic protocols.

Panels of monoclonal antibodies produced against the receptor peptidescan be screened for various properties; i.e., isotype, epitope,affinity, etc. Of particular interest are monoclonal antibodies thatneutralize or modulate the activity of the receptor. Such monoclonalscan be readily identified in receptor activity or signaling assays or intumorigenicity assays. High affinity antibodies are also useful whenimmunoaffinity purification of mutant growth factor receptor, includingEGFR, or constitutively active receptor is desired.

Particularly, the anti-receptor peptide antibody used in the diagnosticmethods of this invention can be an affinity purified polyclonalantibody. More particularly, the antibody is a monoclonal antibody(mAb). In addition, the anti-receptor peptide antibody molecules usedherein may be in the form of Fab, Fab′, F(ab′)₂ or F(v) portions ofwhole antibody molecules. Synthetic, humanized, recombinant or fullyhuman antibodies are particularly preferred and provided.

Therapeutic uses of antibodies are well known within the art. There areseveral ways of using antibodies for therapeutic purposes, for example,as naked antibody in combination with know chemotherapeutic drugs, asradiolabelled antibodies for radioimmuntherapy, or as antibodiesconjugated/coupled with cytotoxic drugs, toxins, or other toxic agents.

Radiolabelled antibodies and fragments thereof, particularlyradioimmunoconjugates, are useful in radioimmunotherapy, particularly asradiolabelled antibodies for cancer therapy. In a still further aspect,the radiolabelled s antibodies and fragments thereof, are useful inradioimmuno-guided surgery techniques, wherein they can identify andindicate the presence and/or location of cancer cells, precancerouscells, tumor cells, and hyperproliferative cells, prior to, during orfollowing surgery to remove such cells.

Immunoconjugates or antibody fusion proteins of the present invention,wherein the antibodies and fragments thereof, of the present inventionare conjugated or attached to other molecules or agents further include,but are not limited to binding members conjugated to a chemical ablationagent, toxin, immunomodulator, cytokine, cytotoxic agent,chemotherapeutic agent or drug.

The antibodies, or antibody fragments, of the current invention may beadministered alone or in combination with other treatments, therapeuticsor agents, either simultaneously or sequentially dependent upon thecondition to be treated. In addition, the present invention contemplatesand includes compositions comprising the antibody or fragment thereof,herein described and other agents or therapeutics such as anti-canceragents or therapeutics, hormones, anti-EGFR agents or antibodies, orimmune modulators. More generally these anti-cancer agents may betyrosine kinase inhibitors or phosphorylation cascade inhibitors,post-translational modulators, cell growth or division inhibitors (e.g.anti-mitotics), or signal transduction inhibitors. Other treatments ortherapeutics may include the administration of suitable doses of painrelief drugs such as non-steroidal anti-inflammatory drugs (e.g.aspirin, paracetamol, ibuprofen or ketoprofen) or opiates such asmorphine, or anti-emetics. The composition can be administered incombination (either sequentially (i.e. before or after) orsimultaneously) with tyrosine kinase inhibitors (including, but notlimited to AG1478 and ZD1839, STI571, OSI-774, SU-6668), doxorubicin,temozolomide, cisplatin, carboplatin, nitrosoureas, procarbazine,vincristine, hydroxyurea, 5-fluoruracil, cytosine arabinoside,cyclophosphamide, epipodophyllotoxin, carmustine, lomustine, and/orother chemotherapeutic agents. Thus, these agents may be anti-EGFRspecific agents, or tyrosine kinase inhibitors such as AG1478, ZD1839,STI571, OSI-774, or SU-6668 or may be more general anti-cancer andanti-neoplastic agents such as doxorubicin, cisplatin, temozolomide,nitrosoureas, procarbazine, vincristine, hydroxyurea, 5-fluoruracil,cytosine arabinoside, cyclophosphamide, epipodophyllotoxin, carmustine,or lomustine. In addition, the composition may be administered withhormones such as dexamethasone, immune modulators, such as interleukins,tumor necrosis factor (TNF), granulocyte macrophage-colony stimulatingfactor (GM-CSF) or other growth factors or cytokines which stimulate theimmune response and reduction or elimination of cancer cells or tumors.An immune modulator such as TNF may be combined together with a memberof the invention in the form of a bispecific antibody recognizing the806 EGFR epitope as well as binding to TNF receptors. The compositionmay also be administered with, or may include combinations along withother anti-EGFR antibodies, including but not limited to the anti-EGFRantibodies 528, 225, SC-03, DR8.3, L8A4, Y10, ICR62 and ABX-EGF.

Previously the use of agents such as doxorubicin and cisplatin inconjunction with anti-EGFR antibodies have produced enhanced anti-tumoractivity (Fan et al, 1993; Baselga et al, 1993). The combination ofdoxorubicin and mAb 528 resulted in total eradication of establishedA431 xenografts, whereas treatment with either agent alone caused onlytemporary in vivo growth inhibition (Baselga et al, 1993). Likewise, thecombination of cisplatin and either mAb 528 or 225 also led to theeradication of well established A431 xenografts, which was not observedwhen treatment with either agent was used (Fan et al, 1993).

As suggested earlier, the diagnostic method of the present inventioncomprises examining a cellular sample or medium by means of an assayincluding an effective amount of an antagonist to a receptor epitopepeptide, such as an anti-receptor peptide antibody, preferably anaffinity-purified polyclonal antibody, and more preferably a mAb. Aspreviously discussed, patients capable of benefiting from this methodinclude those suffering from tumor(s), cancer, a pre-cancerous lesion,or other growth factor receptor condition. Methods for inducinganti-receptor peptide antibodies and for determining and optimizing theability of anti-receptor peptide antibodies to assist in theexamination, isolation, recognition or killing of the target cells,particularly tumor or tumorigenic or cancer cells, are all well-known inthe art.

Methods for producing polyclonal anti-receptor peptide antibodies arewell-known in the art. See U.S. Pat. No. 4,493,795 to Nestor et al. Amonoclonal antibody, typically containing Fab and/or F(ab′)₂ portions ofuseful antibody molecules, can be prepared using the hybridomatechnology described in Antibodies—A Laboratory Manual, Harlow and Lane,eds., Cold Spring Harbor Laboratory, New York (1988), which isincorporated herein by reference. Briefly, to form the hybridoma fromwhich the monoclonal antibody composition is produced, a myeloma orother self-perpetuating cell line is fused with lymphocytes obtainedfrom the spleen of a mammal hyperimmunized with a receptor peptide or animmunogenic fragment thereof.

Splenocytes are typically fused with myeloma cells using polyethyleneglycol (PEG) 6000. Fused hybrids are selected by their sensitivity toHAT. Hybridomas producing a monoclonal antibody useful in practicingthis invention are identified by their ability to immunoreact with thepresent receptor peptides and their ability to inhibit specifiedreceptor peptide or receptor activity in target cells.

A monoclonal antibody useful in practicing the present invention can beproduced by initiating a monoclonal hybridoma culture comprising anutrient medium containing a hybridoma that secretes antibody moleculesof the appropriate antigen specificity. The culture is maintained underconditions and for a time period sufficient for the hybridoma to secretethe antibody molecules into the medium. The antibody-containing mediumis then collected. The antibody molecules can then be further isolatedby well-known techniques.

Media useful for the preparation of these compositions are bothwell-known in the art and commercially available and include syntheticculture media, inbred mice and the like. An exemplary synthetic mediumis Dulbecco's minimal essential medium (DMEM; Dulbecco et al., Virol.8:396 (1959)) supplemented with 4.5 gm/l glucose, 20 mm glutamine, and20% fetal calf serum. An exemplary inbred mouse strain is the Balb/c.

The general methodology for making monoclonal antibodies by hybridomasis well known. Immortal, antibody-producing cell lines can also becreated by techniques other than fusion, such as direct transformationof B lymphocytes with oncogenic DNA, or transfection with Epstein-Barrvirus. See, e.g., M. Schreier et al., “Hybridoma Techniques” (1980);Hammerling et al., “Monoclonal Antibodies And T-cell Hybridomas” (1981);Kennett et al., “Monoclonal Antibodies” (1980); see also U.S. Pat. Nos.4,341,761; 4,399,121; 4,427,783; 4,444,887; 4,451,570; 4,466,917;4,472,500; 4,491,632; 4,493,890.

Methods for producing monoclonal anti-receptor peptide antibodies arealso well-known in the art. See Niman et al., Proc. Natl. Acad. Sci.USA, 80:4949-4953 (1983). Typically, the present receptor peptide or apeptide analog is used either alone or conjugated to an immunogeniccarrier, as the immunogen in the before described procedure forproducing anti-receptor peptide monoclonal antibodies. The hybridomasare screened for the ability to produce an antibody that immunoreactswith the receptor peptide.

Apart from the traditional hybridoma technique there are a number ofother well-known techniques for making monoclonal antibodies.Particularly useful are methods of making fully human antibodies. Onemethod is phage display technology which can be used to select a rangeof human antibodies binding specifically to the antigen using methods ofaffinity enrichment. Phage display has been thoroughly described in theliterature and the construction and screening of phage display librariesare well known in the art, see, e.g., Hoogenboom et al. TrendsBiotechnol., 15:62-70 (1997); Hoogenboom, et al. Immunotechnology 4:1-20(1998); McGregor et al. Mol. Biotechnol, 6:155-62 (1996); and Bird etal., Science, 242:423-426 (1988). Fully human antibodies can also beprepared by immunizing transgenic mice carrying large portions of thehuman immunoglobulin heavy and light chains, with an immunogen. Examplesof such mice are well known within the art, e. g., the Xenomouse®(Abgenix, Inc.) and the HuMAb-Mouse (Medarex, Inc.,), see also U.S. Pat.No. 6,207,418, No. 6,150,584, No. 6,111,166, No. 6,075,181, No.5,922,545, No. 5,545,806 and No. 5,569,825. Antibodies can then beprepared by standard techniques, e. g. standard hybridoma techniques orby phage display.

Moncolonal antibodies derived by hybridoma technique from anotherspecies than human, such as mouse, can be humanized, which means that anon-human antibody gentically engineered to be more human in order toavoid HAMA when infused into humans. The methods humanization ofantibodies are well known within the art, among the more more commonmethods are complementarity-determining region (CDR) grafting andveneering (also known as resurfacing). These methods have beenextensively described in the literature and in patents, see e.g.; King“Applications and Engineering of Monoclonal Antibodies” Taylor &Francis, 1998; U.S. Pat. Nos. 5,225,539; 5,530,101; 5,585,089, 5,859,205and 6,797,492, each incorporated herein by reference.

Another possibility in developing molecules that bind/block/target or insome other way interact with the epitopes and corresponding receptorsdescribed herein, are by making peptides. These peptides could be anyrandom peptide that have an affinity for the eptiopes and they don'tnecessarily have to be of the immunoglobulin family. These peptides areoften isolated by similar techniques as for phage display antibodies(Szardenings, J Recept Signal Transduct Res. 2003; 23(4):307-49). Theuse of peptides from such random peptide libraries are similar toantibodies and antibody fragments.

The present invention also relates to a variety of diagnosticapplications, including methods for detecting the presence of stimulisuch as the earlier referenced polypeptide ligands, by reference totheir ability to elicit the activities which are mediated by the presentreceptor peptides. As mentioned earlier, the receptor peptide can beused to produce antibodies to itself by a variety of known techniques,and such antibodies could then be isolated and utilized as in tests forthe presence of particular ˜ activity in suspect target cells.

As described in detail above, antibody(ies) to the receptor peptide canbe produced and isolated by standard methods including the well knownhybridoma techniques. For convenience, the antibody(ies) to the receptorpeptide will be referred to herein as Ab₁ and antibody(ies) raised inanother species as Ab₂. It will be seen from the below, that acharacteristic property of Ab₂ is that it will react with Ab₁. Forpurposes of this description and claims, Ab₁ will be referred to as aprimary or anti-receptor peptide antibody, and Ab₂ will be referred toas a secondary or anti-Ab₁ antibody.

The presence of exposed receptor epitope peptide in cells can beascertained by the usual immunological procedures applicable to suchdeterminations. A number of useful procedures are known. Three suchprocedures which are especially useful utilize either the receptorpeptide labeled with a detectable label, antibody Ab₁ labeled with adetectable label, or antibody Ab₂ labeled with a detectable label. Theprocedures may be summarized by the following equations wherein theasterisk indicates that the particle is labeled, and “˜” stands for thereceptor peptide:˜*+Ab ₁ =˜*Ab ₁  A.˜+Ab*=˜Ab ₁*  B.˜+Ab ₁ +Ab ₂ *=˜Ab ₁ Ab ₂*  C.

The procedures and their application are all familiar to those skilledin the art and accordingly may be utilized within the scope of thepresent invention. The “competitive” procedure, Procedure A, isdescribed in U.S. Pat. Nos. 3,654,090 and 3,850,752. Procedure C, the“sandwich” procedure, is described in U.S. Pat. Nos. RE 31,006 and4,016,043. Still other procedures are known such as the “doubleantibody,” or “DASP” procedure.

In each instance, the receptor peptide forms complexes with one or moreantibody(ies) or binding partners and one member of the complex islabeled with a detectable label. The fact that a complex has formed and,if desired, the amount thereof, can be determined by known methodsapplicable to the detection of labels.

The labels most commonly employed for these studies are radioactiveelements, enzymes, chemicals which fluoresce when exposed to ultravioletlight, and others.

A number of fluorescent materials are known and can be utilized aslabels. These include, for example, fluorescein, rhodamine, auramine,Texas Red, AMCA blue and Lucifer Yellow. A particular detecting materialis anti-rabbit antibody prepared in goats and conjugated withfluorescein through an isothiocyanate.

The receptor peptide or its binding partner(s) can also be labeled witha radioactive element or with an enzyme. The radioactive label can bedetected by any of the currently available counting procedures. Thepreferred isotope may be selected from ³H, ¹⁴C, ³²P, ³⁵S, ³⁶Cl, ⁵¹Cr,⁵⁷Co, ⁵⁸Co, ⁵⁹Fe, ⁹⁰Y, ¹²⁵I, ¹³¹I, and ¹⁸⁶Re.

Enzyme labels are likewise useful, and can be detected by any of thepresently utilized colorimetric, spectrophotometric,fluorospectrophotometric, amperometric or gasometric techniques. Theenzyme is conjugated to the selected particle by reaction with bridgingmolecules such as carbodiimides, diisocyanates, glutaraldehyde and thelike. Many enzymes which can be used in these procedures are known andcan be utilized. The preferred are peroxidase, β-glucuronidase,β-D-glucosidase, β-D-galactosidase, urease, glucose oxidase plusperoxidase and alkaline phosphatase. U.S. Pat. Nos. 3,654,090;3,850,752; and 4,016,043 are referred to by way of example for theirdisclosure of alternate labeling material and methods.

A particular assay system developed and utilized in accordance with thepresent invention, is known as a receptor assay. In a receptor assay,the material to be assayed is appropriately labeled and then certaincellular test colonies are inoculated with a quantity of both thelabeled and unlabeled material after which binding studies are conductedto determine the extent to which the labeled material binds to the cellreceptors. In this way, differences in affinity between materials can beascertained.

Accordingly, a purified quantity of the receptor peptide may beradiolabeled and combined, for example, with antibodies or otherinhibitors thereto, after which binding studies would be carried out.Solutions would then be prepared that contain various quantities oflabeled and unlabeled uncombined receptor peptide, and cell sampleswould then be inoculated and thereafter incubated. The resulting cellmonolayers are then washed, solubilized and then counted in a gammacounter for a length of time sufficient to yield a standard error of<5%. These data are then subjected to Scatchard analysis after whichobservations and conclusions regarding material activity can be drawn.While the foregoing is exemplary, it illustrates the manner in which areceptor assay may be performed and utilized, in the instance where thecellular binding ability of the assayed material may serve as adistinguishing characteristic.

An assay useful and contemplated in accordance with the presentinvention is known as a “cis/trans” assay. Briefly, this assay employstwo genetic constructs, one of which is typically a plasmid thatcontinually expresses a particular receptor of interest when transfectedinto an appropriate cell line, and the second of which is a plasmid thatexpresses a reporter such as luciferase, under the control of areceptor/ligand complex. Thus, for example, if it is desired to evaluatea compound as a ligand for a particular receptor, one of the plasmidswould be a construct that results in expression of the receptor in thechosen cell line, while the second plasmid would possess a promoterlinked to the luciferase gene in which the response element to theparticular receptor is inserted. If the compound under test is anagonist for the receptor, the ligand will complex with the receptor, andthe resulting complex will bind the response element and initiatetranscription of the luciferase gene. The resulting chemiluminescence isthen measured photometrically, and dose response curves are obtained andcompared to those of known ligands. The foregoing protocol is describedin detail in U.S. Pat. No. 4,981,784 and PCT International PublicationNo. WO 88/03168, for which purpose the artisan is referred.

In a further embodiment of this invention, commercial test kits suitablefor use by a medical specialist may be prepared to determine thepresence or absence of abnormal growth factor receptor or exposedreceptor epitope peptide in suspected target cells. In accordance withthe testing techniques discussed above, one class of such kits willcontain at least the labeled receptor peptide or its binding partner,for instance an antibody specific thereto, and directions, of course,depending upon the method selected, e.g., “competitive,” “sandwich,”“DASP” and the like. The kits may also contain peripheral reagents suchas buffers, stabilizers, etc.

Accordingly, a test kit may be prepared for the demonstration of thepresence or capability of cells for predetermined abnormal growth factorreceptor, including EGFR, activity, comprising:

(a) a predetermined amount of at least one labeled immunochemicallyreactive component obtained by the direct or indirect attachment of thepresent receptor peptide or a specific binding partner thereto, to adetectable label;

(b) other reagents; and

(c) directions for use of said kit.

More specifically, the diagnostic test kit may comprise:

(a) a known amount of the receptor peptide as described above (or abinding partner) generally bound to a solid phase to form animmunosorbent, or in the alternative, bound to a suitable tag, or pluralsuch end products, etc. (or their binding partners) one of each;

(b) if necessary, other reagents; and

(c) directions for use of said test kit.

In a further variation, the test kit may be prepared and used for thepurposes stated above, which operates according to a predeterminedprotocol (e.g. “competitive,” “sandwich,” “double antibody,” etc.), andcomprises:

(a) a labeled component which has been obtained by coupling the receptorpeptide to a detectable label;

(b) one or more additional immunochemical reagents of which at least onereagent is a ligand or an immobilized ligand, which ligand is selectedfrom the group consisting of:

-   -   (i) a ligand capable of binding with the labeled component (a);    -   (ii) a ligand capable of binding with a binding partner of the        labeled component (a);    -   (iii) a ligand capable of binding with at least one of the        component(s) to be determined; and    -   (iv) a ligand capable of binding with at least one of the        binding partners of at least one of the component(s) to be        determined; and

(c) directions for the performance of a protocol for the detectionand/or determination of one or more components of an immunochemicalreaction between the receptor peptide and a specific binding partnerthereto.

In accordance with the above, an assay system for screening potentialdrugs effective to modulate the activity of the receptor peptide, or anantibody thereto may be prepared. The receptor peptide or antibody maybe introduced into a test system, and the prospective drug may also beintroduced into the resulting cell culture, and the culture thereafterexamined to observe any changes in the growth factor receptor activityof the cells, due either to the addition of the prospective drug alone,or due to the effect of added quantities of the known receptor peptide,or an antibody thereto.

Compositions

The present invention further contemplates therapeutic compositionsuseful in practicing the therapeutic methods of this invention. Asubject therapeutic composition includes, in admixture, apharmaceutically acceptable excipient (carrier) and one or more of areceptor peptide, particularly selected from a peptide having a sequenceof any of SEQ ID NOS: 1-14, or immunogenic fragment thereof, asdescribed herein as an active ingredient.

The preparation of therapeutic compositions which contain polypeptides,analogs or active fragments as active ingredients is well understood inthe art. Typically, such compositions are prepared as injectables,either as liquid solutions or suspensions, however, solid forms suitablefor solution in, or suspension in, liquid prior to injection can also beprepared. The preparation can also be emulsified. The active therapeuticingredient is often mixed with excipients which are pharmaceuticallyacceptable and compatible with the active ingredient. Suitableexcipients are, for example, water, saline, dextrose, glycerol, ethanol,or the like and combinations thereof. In addition, if desired, thecomposition can contain minor amounts of auxiliary substances such aswetting or emulsifying agents, pH buffering agents which enhance theeffectiveness of the active ingredient.

A polypeptide, analog or active fragment can be formulated into thetherapeutic composition as neutralized pharmaceutically acceptable saltforms. Pharmaceutically acceptable salts include the acid addition salts(formed with the free amino groups of the polypeptide or antibodymolecule) and which are formed with inorganic acids such as, forexample, hydrochloric or phosphoric acids, or such organic acids asacetic, oxalic, tartaric, mandelic, and the like. Salts formed from thefree carboxyl groups can also be derived from inorganic bases such as,for example, sodium, potassium, ammonium, calcium, or ferric hydroxides,and such organic bases as isopropylamine, trimethylamine, 2-ethylaminoethanol, histidine, procaine, and the like.

The therapeutic receptor peptide or immunogenic fragment-containingcompositions may be administered orally, intramuscularly,intraperitoneally or intravenously, as by injection or administration ofa unit dose, for example. The term “unit dose” when used in reference toa therapeutic composition of the present invention refers to physicallydiscrete units suitable as unitary dosage for humans, each unitcontaining a predetermined quantity of active material calculated toproduce the desired therapeutic effect in association with the requireddiluent; i.e., carrier, or vehicle. The therapeutic receptor peptide orimmunogenic fragment-containing compositions may be administeredmultiply in series, as in an immunization schedule.

The compositions are administered in a manner compatible with the dosageformulation, and in a therapeutically effective amount. The quantity tobe administered depends on the subject to be treated, capacity of thesubject's immune system to utilize the active ingredient, and degree ofinhibition or neutralization of growth factor receptor binding andsignaling capacity desired. Precise amounts of active ingredientrequired to be administered depend on the judgment of the practitionerand are peculiar to each individual. However, suitable dosages may rangefrom about 0.1 to 20, preferably about 0.5 to about 10, and morepreferably one to several, milligrams of active ingredient per kilogrambody weight of individual per day and depend on the route ofadministration. Suitable regimes for initial administration and boostershots are also variable, but are typified by an initial administrationfollowed by repeated doses at one or more hour intervals by a subsequentinjection or other administration. Alternatively, continuous intravenousinfusion sufficient to maintain concentrations of ten nanomolar to tenmicromolar in the blood are contemplated.

The therapeutic compositions may further include an effective amount ofthe receptor peptide, or antibody thereto, and one or more of thefollowing active ingredients: an anti-mitotic, a chemotherapeutic agent,an immunomodulator.

Nucleic Acids

Another feature of this invention is the expression of DNA sequencesencoding the receptor peptides disclosed herein. As is well known in theart, DNA sequences may be expressed by operatively linking them to anexpression control sequence in an appropriate expression vector andemploying that expression vector to transform an appropriate unicellularhost. Such operative linking of a DNA sequence of this invention to anexpression control sequence, of course, includes, if not already part ofthe DNA sequence, the provision of an initiation codon, ATG, in thecorrect reading frame upstream of the DNA sequence.

A wide variety of host/expression vector combinations may be employed inexpressing the DNA sequences of this invention. Useful expressionvectors, for example, may consist of segments of chromosomal,non-chromosomal and synthetic DNA sequences. Suitable vectors includederivatives of SV40 and known bacterial plasmids, e.g., E. coli plasmidscol E1, pCR1, pBR322, pMB9 and their derivatives, plasmids such as RP4;phage DNAS, e.g., the numerous derivatives of phage λ, e.g., NM989, andother phage DNA, e.g., M13 and filamentous single stranded phage DNA;yeast plasmids such as the 2μ plasmid or derivatives thereof; vectorsuseful in eukaryotic cells, such as vectors useful in insect ormammalian cells; vectors derived from combinations of plasmids and phageDNAs, such as plasmids that have been modified to employ phage DNA orother expression control sequences; and the like.

Any of a wide variety of expression control sequences—sequences thatcontrol the expression of a DNA sequence operatively linked to it—may beused in these vectors to express the DNA sequences of this invention.Such useful expression control sequences include, for example, the earlyor late promoters of SV40, CMV, vaccinia, polyoma or adenovirus, the lacsystem, the trp system, the TAC system, the TRC system, the LTR system,the major operator and promoter regions of phage λ, the control regionsof fd coat protein, the promoter for 3-phosphoglycerate kinase or otherglycolytic enzymes, the promoters of acid phosphatase (e.g., Pho5), thepromoters of the yeast α-mating factors, and other sequences known tocontrol the expression of genes of prokaryotic or eukaryotic cells ortheir viruses, and various combinations thereof.

A wide variety of unicellular host cells are also useful in expressingthe DNA sequences of this invention. These hosts may include well knowneukaryotic and prokaryotic hosts, such as strains of E. coli,Pseudomonas, Bacillus, Streptomyces, fungi such as yeasts, and animalcells, such as CHO, R1.1, B-W and L-M cells, African Green Monkey kidneycells (e.g., COS 1, COS 7, BSC1, BSC40, and BMT10), insect cells (e.g.,Sf9), and human cells and plant cells in tissue culture.

It will be understood that not all vectors, expression control sequencesand hosts will function equally well to express the DNA sequences ofthis invention. Neither will all hosts function equally well with thesame expression system. However, one skilled in the art will be able toselect the proper vectors, expression control sequences, and hostswithout undue experimentation to accomplish the desired expressionwithout departing from the scope of this invention. For example, inselecting a vector, the host must be considered because the vector mustfunction in it. The vector's copy number, the ability to control thatcopy number, and the expression of any other proteins encoded by thevector, such as antibiotic markers, will also be considered.

In selecting an expression control sequence, a variety of factors willnormally be considered. These include, for example, the relativestrength of the system, its controllability, and its compatibility withthe particular DNA sequence or gene to be expressed, particularly asregards potential secondary structures. Suitable unicellular hosts willbe selected by consideration of, e.g., their compatibility with thechosen vector, their secretion characteristics, their ability to foldproteins correctly, and their fermentation requirements, as well as thetoxicity to the host of the product encoded by the DNA sequences to beexpressed, and the ease of purification of the expression products.

Considering these and other factors a person skilled in the art will beable to construct a variety of vector/expression control sequence/hostcombinations that will express the DNA sequences of this invention onfermentation or in large scale animal culture.

It is further intended that peptide analogs may be prepared fromnucleotide sequences of the protein complex/subunit derived within thescope of the present invention. Analogs, such as fragments, may beproduced, for example, by proteolytic digestion, including pepsindigestion, of the peptides. Other analogs, such as muteins, can beproduced by standard site-directed mutagenesis of receptor peptidecoding sequences. Analogs exhibiting “receptor epitope peptide activity”such as small molecules, whether functioning as promoters or inhibitors,may be identified by known in vivo and/or in vitro assays.

As mentioned above, a DNA sequence encoding the receptor peptide(s) canbe prepared synthetically rather than cloned. The DNA sequence can bedesigned with the appropriate codons for the receptor peptide amino acidsequence. In general, one will select preferred codons for the intendedhost if the sequence will be used for expression. The complete sequenceis assembled from overlapping oligonucleotides prepared by standardmethods and assembled into a complete coding sequence. See, e.g., Edge,Nature, 292:756 (1981); Nambair et al., Science, 223:1299 (1984); Jay etal., J. Biol. Chem., 259:6311 (1984).

Synthetic DNA sequences allow convenient construction of genes whichwill express receptor peptide analogs or “muteins”. Alternatively, DNAencoding muteins can be made by site-directed mutagenesis of nativegrowth factor receptor genes or cDNAs, and muteins can be made directlyusing conventional polypeptide synthesis.

A general method for site-specific incorporation of unnatural aminoacids into proteins is described in Christopher J. Noren, Spencer J.Anthony-Cahill, Michael C. Griffith, Peter G. Schultz, Science,244:182-188 (April 1989). This method may be used to create analogs withunnatural amino acids.

Antigens and Vaccines

The characterization of tumour antigens recognised by T cells hasrevolutionized the cancer-vaccine approach, providing for the first timethe opportunity to immunise patients against cancer by usingwell-defined antigens. Because melanoma is one of the prototypicimmunogenic tumours, a number of early-phase clinical trials have beenconducted on melanoma. Some tumour regressions have been documented,mainly for patients with metastatic disease. Recent advances include newtools for monitoring the anti-cancer immune response and the developmentof adjuvants aimed at inducing a robust anti-melanoma immune response.

Prostate cancer is the second leading cause of cancer death in males inthe USA. Vaccine strategies represent a novel therapeutic approach. Onepotential target for a prostate cancer vaccine is prostate-specificantigen (PSA), due to its restricted expression in prostate cancer andnormal prostatic epithelial cells. A number of PSA-specific epitopeshave been identified that can activate cytotoxic T-lymphocytes (CTLs)and in turn lead to the killing of tumor targets by the peptide-specificCTLs. Strategies have now been employed in clinical trials usingRNA-pulsed dendritic cell vaccines, recombinant protein vaccines, andrecombinant viral vector delivery of vaccines. Newer approachesincorporating costimulatory molecules that enhance Tcell activation arealso being investigated.

Dendritic cells (DCs) are potent antigen-presenting cells that have theability to stimulate primary T cell anti-tumor immune responses inanimals and humans. Since the first published clinical trial ofdendritic cell vaccination in 1995, 98 studies describing more than 1000vaccinees have been published in peer-reviewed medical journals orpresented at the annual meetings of the American Society for ClinicalOncology, the American Association of Cancer Research, or the AmericanSociety of Hematology. Trials have been performed in 15 countries.Trials included patients with more than two dozen tumor types; mosttrials studied patients with malignant melanoma, prostate cancer,colorectal carcinoma, or multiple myeloma, using autologous DCs pulsedwith synthetic antigens or idiotype antibodies. The DC vaccines werealso prepared by pulsing DCs with tumor lysates or RNA, by transfectionwith tumor DNA, or by creating tumor cell/DC fusions. Various approachesto vaccine cell numbers, length of vaccine program, site of vaccination,frozen preservation of vaccine, and use of a maturation step for DCswere used. Adverse effects associated with DC vaccination were uncommon;most were mild and self-limited and none were serious. Clinicalresponses were observed in approximately half the trials. The DCvaccination may provide a safe approach to cancer immunotherapy that canovercome the limited reach and immunogenicity of peptide vaccines.

After successful studies in mice and monkeys, Gonzales et al (Gonzales,G et al (2003) Annals Oncol 14:461-466) reported human studies ofvaccination with the EGFR ligand, EGF, coupled to a carrier protein, theP64K Neisseria meningitides outer membrane recombinant protein, inpatients with advanced stage non-small-cell-lung cancer (NSCLC). Bettersurvival times were observed in patients with a good anti-EGF antibodyresponse.

Synthetic antigens, including vaccines, may be prepared by chemicallysynthesizing the receptor peptides of the present invention, optionallyincluding other tumor antigens. These peptides, peptide carriercombinations, lipid derivatives of such peptides as well as tumorantigens, may be used either individually or combined as a cocktail, andformulated with an adjuvant to provide an immunogenic composition. Ascontemplated herein, an antigen may be covalently bonded to a glycolipidanalog to provide a discrete molecule which exhibits an enhancedadjuvanting effect on the antigen which is greater than the adjuvantingeffect attainable in the absence of such covalent bonding. Thesecompositions can be used to immunize mammals, for example, by theintramuscular or parenteral routes, or by delivery to mucosal surfacesusing microparticles, capsules, liposomes and targeting molecules, suchas toxins and antibodies.

Vaccines containing peptides are generally well known in the art, asexemplified by U.S. Pat. Nos. 4,601,903; 4,599,231; 4,599,230; and4,596,792; all of which references are incorporated herein by reference.The use of peptides in vivo may first require their chemicalmodification since the peptides themselves may not have a sufficientlylong serum and/or tissue half-life and/or sufficient immunogenicity. Inaddition, it may be advantageous to modify the peptides in order toimpose a conformational restraint upon them. This might be useful, forexample, to mimic a naturally-occurring conformation of the peptide inthe context of the native protein in order to optimize the effectorimmune responses that are elicited.

This invention provides an immunogenic composition comprising an amountof the receptor peptide, or immunogenic fragments thereof andcombinations thereof. In one embodiment the receptor peptide is selectedfrom SEQ ID NOS: 1-14.

This invention provides a method of stimulating or enhancing anantigen-specific cell-mediated immune response which comprisesadministering to a subject an amount of a receptor peptide, orimmunogenic fragment thereof, and a suitable adjuvant.

This invention provides a method of treating a subject with a tumor orcancer comprising administering to a subject an amount of the receptorpeptide and adjuvant composition of the present invention as animmunomodulator, and a suitable carrier or diluent. In particular, asubject having cancer may be treated with the receptor peptide-adjuvantcomposition. Such cancers include but are not limited to head and neckcancer, breast cancer, lung cancer, ovarian cancer, bladder cancer,laryngeal cancer, squamous cell carcinoma, or prostate tumors andglioma.

Further the subject may be treated with the receptor peptide orimmunogenic composition thereof in combination with chemotherapeutic,chemopreventive, or radiation therapy. It is contemplated by thisinvention that the receptor peptide composition could be used inconjunction with chemo- or radiotherapeutic intervention. In anotherembodiment, treatment with the receptor peptide composition may precedeor follow the DNA damaging agent treatment by intervals ranging fromminutes to weeks. Protocols and methods are known to those skilled inthe art. DNA damaging agents or factors are known to those skilled inthe art and means any chemical compound or treatment method that inducesDNA damage when applied to a cell. Such agents and factors includeradiation and waves that induce DNA damage such as, gamma-irradiation,X-rays, UV-irradiation, microwaves, electronic emissions, and the like.A variety of chemical compounds, also described as “chemotherapeuticagents”, function to induce DNA damage, all of which are intended to beof use in the combined treatment methods disclosed herein.Chemotherapeutic agents contemplated to be of use, include, e.g.,adriamycin, 5-fluorouracil (5FU), etoposide (VP-16), camptothecin,actinomycin-D, mitomycin C, cisplatin (CDDP) and even hydrogen peroxide.Combinations of one or more DNA damaging agents may be used with theEHA, whether radiation-based or actual compounds, such as the use ofX-rays with cisplatin or the use of cisplatin with etoposide. Otherneoplastic or toxic agents include but are not limited: 5-fluorouracil,methotrexate and adriamycin which may be linked in each case to, forexample, a cephalosporin (see WO-A94 01 137 and EP-A-0 382 411) orcephalosporin mustards (see EP-A-O 484 870).

The receptor peptide or immunogenic compositions may be prepared asinjectables, as liquid solutions or emulsions. The antigens andimmunogenic compositions may be mixed with physiologically acceptablecarriers which are compatible therewith. These may include water,saline, dextrose, glycerol, ethanol and combinations thereof. Thevaccine may further contain auxiliary substances, such as wetting oremulsifying agents or pH buffering agents, to further enhance theireffectiveness. Vaccines may be administered by injection subcutaneouslyor intramuscularly.

Alternatively, the immunogenic compositions formed according to thepresent invention, may be formulated and delivered in a manner to evokean immune response at mucosal surfaces. Thus, the immunogeniccomposition may be administered to mucosal surfaces by, for example, thenasal or oral (intragastric) routes. Alternatively, other modes ofadministration including suppositories may be desirable. Forsuppositories, binders and carriers may include, for example,polyalkylene glycols and triglycerides. Oral formulations may includenormally employed excipients, such as pharmaceutical grades ofsaccharine, cellulose and magnesium carbonate.

The modes of administration may comprise the use of any suitable meansand/or methods for delivering the adjuvant or adjuvant-containingvaccine to a corporeal locus of the host animal where the adjuvant andassociated antigens are immumostimulatively effective. Delivery modesmay include, without limitation, parenteral administration methods, suchas paracancerally, transmucosally, transdermally, intramuscularly,intravenously, intradermally, subcutaneously, intraperitonealy,intraventricularly, intracranially and intratumorally.

The invention may be better understood by reference to the followingnon-limiting Examples, which are provided as exemplary of the invention.The following examples are presented in order to more fully illustratethe preferred embodiments of the invention and should in no way beconstrued, however, as limiting the broad scope of the invention.

Example 1

The epidermal growth factor receptor (EGFR) is over-expressed in manyepithelial cancers, an observation often correlated with poor clinicaloutcome. Over-expression of the EGFR is commonly caused by EGFR geneamplification and is sometimes associated with expression of a variantEGFR (de2-7 EGFR or EGFRvIII) bearing an internal deletion in itsextracellular domain. MAb 806 is a novel EGFR antibody with significantanti-tumor activity that recognizes both the de2-7 EGFR and a subset ofthe wild type (wt) EGFR when over-expressed, but does not bind the wtEGFR expressed in normal tissues. Despite only binding to a lowproportion of the wt EGFR expressed in A431 tumor cells (˜10%), mAb 806displays robust anti-tumor activity against A431 xenografts grown innude mice. To elucidate the mechanism leading to its unique specificityand mode of anti-tumor activity, we have determined the EGFR bindingepitope of mAb 806. Analysis of mAb 806 binding to EGFR fragments eitherexpressed on the surface of yeast, or in an immunoblot format,identified a disulfide-bonded loop (amino acids 287-302) that appearedto contain the mAb 806 epitope. Indeed, mAb 806 bound with apparent highaffinity (˜30 nM) to a synthetic EGFR peptide corresponding to theseamino acids. Analysis of the EGFR structure indicates that thisdisulfide-bonded loop is only available for mAb 806 binding in atransitional form of the receptor that occurs, as the EGFR changes fromthe inactive tethered conformation to a ligand-bound activeconformation. It would appear that mAb 806 binds this small proportionof transient receptors preventing their activation, which in turngenerates a strong anti-tumor effect. Finally, our observations suggeststhat the generation of antibodies to transitional forms of growth factorreceptors may represent a novel way of reducing normal tissue targetingyet retaining anti-tumor activity.

Introduction

The epidermal growth factor receptor (EGFR) is a 170 kDa membrane boundtyrosine kinase that is responsible for directing the proliferation anddifferentiation of many different cell types (1, 2). Over-expression ofthe EGFR has been observed in many epithelial tumors, with increasedEGFR expression levels usually correlating with poor clinical outcome(3-5). Over-expression of the receptor is often caused by amplificationof the EGFR gene, an event also linked with EGFR mutation (6). The mostcommon EGFR mutation is an extracellular truncation of the EGFR known asthe de2-7 EGFR (or EGFRvIII), which is frequently expressed in glioma(6-8). This truncation results in the removal of 267 amino acids fromthe extracellular domain of the EGFR and the insertion of a novelglycine, which generates an unique junctional peptide near theN-terminal of the de2-7 EGFR (6-8). While the de2-7 EGFR is unable tobind any known ligand it does display low levels of constitutiveactivation and enhances the tumorgenicity of glioma and breast cellswhen grown as xenografts in nude mice (9-11).

Inhibition of the EGFR is a rational strategy for the development of newcancer therapeutics (12). Potential therapeutics include anti-EGFRantibodies (13) and small molecular weight tyrosine kinase inhibitors(14) of the EGFR. A number of antibodies directed to the extra-cellulardomain of the EGFR have now been tested in the clinic including EMD55900 (15), ABX-EGF (16) and C225 (Cetuximab) (17), all of which havedisplayed some anti-tumor activity in patients. The most clinicallyadvanced of these is C225, which is currently being tested in PhaseII/III clinical trials for the treatment of head and neck, colorectaland non-small cell lung carcinomas and has been recently approved foruse in Europe (18). It has been presumed that the anti-tumor activity ofthese antibodies is primarily related to their ability to block ligandbinding but other anti-tumor mechanisms such as immune effectorfunction, receptor down-regulation, induction of inappropriate signalingand interference with receptor dimerization and/or oligomerization couldalso play a role. One limitation of antibodies targeting the wild type(wt) EGFR is that they show significant uptake in normal tissue such asthe liver and skin (19, 20). At present targeting of the normal EGFRappears to cause manageable side effects such as skin rash, however ifthese anti-EGFR antibodies were coupled to cytotoxic agents orradioisotopes significant liver damage would be expected.

The mAb 806 was raised against mouse fibroblast cells expressing thede2-7 EGFR and does not bind normal tissue expressing the wt EGFR,making it an attractive candidate for cancer therapy (21). Unlike otherde2-7 EGFR specific antibodies, which are all specific to the uniquede2-7 EGFR junctional peptide (24-26), mAb 806 recognizes a differentand unknown epitope (27). Indeed, mAb 806 can robustly bind the wt EGFRfollowing denaturation of the EGFR by immunoblotting or even coating onthe surface of ELISA plates. While mAb 806 recognizes a large fractionof the de2-7 EGFR, it also binds some of the wt EGFR in cells whichover-express the receptor (27). Scatchard analysis has revealed that mAb806 binds ˜50% of the de2-7 EGFR recognized by mAb DH8.3, an antibodyspecific for the de2-7 EGFR junctional peptide (27). In contrast, mAb806 bound <10% of the wt EGFR over-expressed on A431 cells when comparedwith the wt EGFR specific mAb 528. Importantly mAb 806 does not bind tonormal tissue expressing the wt EGFR. Interestingly, mAb 806 alsopreferentially recognizes the high mannose form of the EGFR normallylocated within the endoplasmic reticulum. When used as a single agent,mAb 806 demonstrated significant anti-tumor activity against humanxenografts expressing either the de2-7 or amplified EGFR. Determinationof the mAb 806 binding epitope would be important for understanding itsmechanism of action, as well as providing a general strategy fordeveloping tumor-specific antibodies. Using two independent approacheswe now identify the epitope recognized by mAb 806. Taking advantage ofthe recently described crystal structure for the EGFR, we were also ableto explain the unique specificity of mAb 806 and how it mediates itsanti-tumor activity.

Experimental Procedures

Antibodies

The IgG2b monoclonal antibody 806 and IgG2a mAb528 specific for the EGFRwere produced and purified in the Biological Production Facility (LudwigInstitute for Cancer Research, Melbourne) as previously described (27,28).

Expression Vectors

The expression vectors pEE14/sEGFR501 and pEE14/sEGFR513 have beendescribed previously (29) and encode the signal peptide and first 501and 513 amino acids, respectively, of the EGFR ectodomain followed by ac-myc epitope tag, all transcribed under the control of the humancytomegalovirus immediate early promoter. The expression vectorpEE14/sEGFR310-501 contains cDNA encoding the signal peptide of the EGFRfused in-frame to amino acid residues 310-501 of the ectodomain,terminating with the epitope tag.

A series of overlapping EGFR c-myc tagged ectodomain fragments, startingat residues 274, 282, 290 and 298 and all terminating at amino acid 501,were generated by PCR. Following sequence analysis, the fragments werecloned in-frame into the 3′ end of the human growth hormone (GH) geneexpressed from the mammalian expression vector, pSGHVO (30).Double-stranded oligonucleotides spanning residues 278-286 and 285-293were cloned in-frame into the same vector between GH and the c-myc tag.

Transfections

Human 293T embryonic kidney fibroblasts were maintained in Dulbecco'sModified Eagle Medium (DMEM) plus 10% foetal calf serum (FCS). The dayprior to transfection, cells were seeded at 8×10⁵ per well in 6-welltissue culture plates containing 2 ml of media. Cells were transfectedwith 3-4 μg of plasmid DNA complexed with Lipofectamine 2000(Invitrogen) according to the manufacturer's instructions. Twenty fourto 48 hours after transfection, cell cultures were aspirated and cellmonolayers lysed in 250 μl of lysis buffer (1% Triton X-100, 10%glycerol, 150 mM NaCl, 50 mM HEPES pH 7.4, 1 mM EGTA and CompleteProtease Inhibitor mix (Roche).

The CR1-loop (dimerization arm) deletion was generated by removing aminoacid 244-259 and replacing them with a single alanine residue asdescribed. 293T cells were transfected with this construct and stabletransfectants selected in the presence of geneticin.

Western Blotting

Aliquots of cell lysate (10-15 μl) were mixed with SDS sample buffercontaining 1.5% β-mercaptoethanol, denatured by heating for 5 minutes at100° C. and electrophoresed on 10% NuPAGE Bis-Tris polyacrylamide gels(Invitrogen). Samples were then electro-transferred to nitrocellulosemembranes which were rinsed in TBST buffer (10 mM Tris-HCI, pH 8.0, 100mM NaCl and 0.1% Tween-20) and blocked in TBST containing 2.5% skim milkfor 30 minutes at room temperature. Membranes were incubated overnightat 4° C. with 0.5 μg/ml of mAb 806 in blocking buffer. Parallelmembranes were probed overnight with mAb 9B11 (1:5000, Cell SignallingTechnology) to detect the c-myc epitope. Filters were washed in TBST,and incubated in blocking buffer containing horseradishperoxidase-conjugated rabbit anti-mouse immunoglobulin (Biorad) at a1:5000 dilution for 2 hours at room temperature. Blots were then washedin TBST, and developed using autoradiographic film following incubationwith Western Pico Chemilumiscent Substrate (Pierce). For peptidecompetition experiments, blots were probed for 1 hour at roomtemperature with Mab 806 in the presence of a 100-fold molar excess ofcompeting peptide. Following chemiluminescent detection, blots werere-probed with 9B 11.

Yeast Surface Display of EGFR Fragments

The pCT yeast display plasmids, modified to contain the appropriategenes encoding for the EGFR fragments, were transformed into the yeaststrain EBY100 (32) by electroporation (33) using a Bio-Rad (Richmond,Calif.) Gene Pulser Transfection Apparatus. The plasmid contains a trp⁺marker that can be used to select for yeast which have incorporated theDNA into their genome. Expression of EGFR proteins on the yeast cellsurface was performed as previously described (Boder and Wittrup, 2000).Briefly, transformed colonies were grown at 30° C. in minimal mediacontaining yeast nitrogen base, caseamino acids, dextrose, and phosphatebuffer pH 7.4, on a shaking platform for approximately one day until anOD₆₀₀ of 5-6 was reached. Yeast cells were then induced for proteindisplay by transferring to minimal media containing galactose, andincubated with shaking at 30° C. for 24 hr. Cultures were then stored at4° C. until analysis.

Antibody Labeling Experiments on the Yeast Cell Surface

Raw ascites fluid containing the c-myc monoclonal antibody 9E10 wasobtained from Covance (Richmond, Calif.). 1×10⁶ yeast cells were washedwith FACS buffer (PBS containing 1 mg/ml BSA) and incubated with eitheranti-c-myc ascites (1:50 dilution), or human EGFR monoclonal antibody(10 μg/ml) in a final volume of 50 μl, for 1 hr at 4° C. The cells werethen washed with ice cold FACS buffer and incubated withphycoerythrin-labeled anti-mouse IgG (1:25 dilution), in a final volumeof 50 μl for 1 hr at 4° C., protected from light. After washing theyeast cells with ice-cold FACS buffer, fluorescence data was obtainedwith a Coulter Epics XL flow cytometer (Beckman-Coulter), and analyzedwith WinMDI cytometry software (J. Trotter, Scripps University). Fordetermination of linear versus conformational epitopes, yeast cells wereheated at 80° C. for 30 min, then chilled on ice 20 min prior tolabeling with antibodies.

EGFR-Derived Peptides

Peptides (₂₈₇CGADSYEMEEDGVRKC₃₀₂ (SEQ ID NO: 1), ₂₈₇CGADSYEMEEDGVRK₃₀₁(SEQ ID NO:2) and ₂₈₇CGADSYEMEEDG₂₉₈ (SEQ ID NO: 15)) containing theputative mAb 806 epitope was synthesized using standard F_(moc)chemistry and verified mass spectral analysis. Cyclised peptide wasprepared by the overnight aerial oxidation of a dilute peptide solutionin alkaline conditions. Linear (reduced) peptide was prepared bydissolving the synthesised peptide in aqueous 10 mM HCl. A sample of the287-302 peptide was reacted with cyanogen bromide in 70% formic underanaerobic to generate fragments corresponding to the N- and C-terminalpeptides. The peptides were separated by HPLC on a C18 Vydac columnusing an acetonitrile gradient in the presence of 0.1% trifluoraceticacid (TFA). The authenticity of the peptides were subsequentlycharacterised by mass spectrometry and N-terminal sequencing. A sampleof S-carboxymethylated peptide (SCM-peptide) was produced by reactingthe peptide with dithiothreitol in 0.5 M sodium bicarbonate pH 8.6followed by the addition of iodoacetamide. The SCM-peptide wassubsequently purified by RP-HPLC as described above.

ELISA Assay

The wells of white polystyrene 96-well plates (Greiner Lumitrac 600)were coated with 2 μg/ml 501-Fc, a variant form of sEGFR501 fused to thehuman Fc constant region (T. Adams, unpublished results), in 10 mMsodium citrate pH 5.9 and then blocked with 0.5% chicken ovalbumin inTBS. After washing with TBST, solutions (100 μl/well) of 0.5 μg/mlmAb806 and varying concentrations of peptides were added to the wells.Plate-bound mAb 806 was detected using goat anti-mouseimmunoglobulin-HRP (BioRad) and Western Pico Chemilumiscent Substrate(Pierce) and quantitated using a Wallac Victor 1420 counter (PerkinElmer). In some assays 96-well plates were coated with the 1-501 EGFRand used to analyse mAb 806 binding as previously described (Johns et.al. Intl. J. Cancer 98: 398-408, 2002).

Surface Plasmon Resonance (BIAcore)

A BIAcore 3000 was used for all experiments. The peptides containing theputative mAb 806 epitope were immobilised on a CM5 sensor chip usingamine or thiol-disulphide exchange coupling at a flow rate of 5 μl/min(34). The 806 antibody was passed over the sensor surface at a flow rateof 5 μl/min at 25° C. The surfaces were generated between runs byinjecting 10 mM HCl at a flow rate of 10 μl/min.

Flow Cytometry Analysis

Cultured 293 cells expressing different EGFR constructs were analysedfor EGFR expression using mAb 528 and 806. 1×10⁶ cells were incubatedwith 5 μg/ml of primary antibody, in PBS containing 1% HSA for 30 min at4° C. After washing with PBS/1% HSA, cells were incubated a further 30min with FITC-coupled goat anti-mouse antibody at 4° C. (1:100 dilution;Calbiochem, San Diego, Calif.). Cells were then analysed on an EpicsElite ESP (Beckman Coulter, Hialeah, Fla.) by observing a minimum of5,000 events and analysed using EXPO (version 2) for Windows.

Results

Identification of the mAb 806 Epitope by Immunoblotting of EGFRFragments

In order to determine the broad location of the mAb 806 epitope, the1-513 and 310-501 c-myc tagged EGFR fragments were separated by SDS-PAGEand immunoblotted with mAb 806. While mAb 806 showed strong reactivitywith the 1-513 fragment, it did not bind at all to the 310-501 segmentof the EGFR (FIG. 1, left panel). The 310-501 fragment was present onthe membrane as it could be detected using mAb 9B11 which is specificfor the c-myc tag (FIG. 1, right panel). In other experiments, weestablished that mAb 806 also bound the sEGFR501 fragment in westernblots (data not shown). Given that mAb 806 binds the de2-7 EGFR (27),which has amino acids 6-273 deleted, we concluded that the mAb 806epitope must be contained within residues 274-310 or 501-513. Todelineate the epitope of mAb 806 we expressed a series of c-myc-taggedEGFR fragments all terminating at amino acid 501. The mAb 806 reactedwith both the 274-501 and 282-501 EGFR fragments, but failed to bind tosegments commencing at amino acid 290 or 298 (FIG. 1, left panel). Thepresence of all the EGFR constructs was confirmed using the c-mycantibody (FIG. 1, right panel). Thus, the mAb 806 epitope must becontained within amino acids 282-310. Furthermore, while the epitopecould extend beyond amino acid 290, the 282-290 region must contain someof the amino acids residues critical for mAb 806 reactivity in thisparticular immunoblotting assay.

Identification of the mAb 806 Epitope by Display of EGFR Fragments onthe Surface of Yeast

We used a second independent approach to determine the mAb 806 epitope.Fragments encompassing different domains of the EGFR were expressed onthe surface of yeast and tested for mAb 806 binding by FACS. The mAb 806recognized both the 1-621 and 1-501 fragments expressed on the surfaceof yeast (FIG. 2A). The mAb 806 also bound the 273-621 EGFR fragmentthat corresponds to the extracellular domain of the de2-7 EGFR (FIG.2A). In contrast, mAb 806 could not recognize the 294-543 or 475-621EGFR fragments (FIG. 2A), clearly demonstrating that at least some ofthe mAb 806 epitope must be contained within the region between aminoacids 274-294 (c.f. amino acids 282-290 identified above). Given thatthese two disparate approaches identified the same region as criticalfor mAb 806 binding, we were confident that this section of the EGFRmust contain an energetically important portion of the mAb 806 epitope.Interestingly, heat denaturation at 80° C. of the 1-501 epitope had noeffect on mAb 806 binding suggesting that the epitope is linear ratherthan conformational (FIG. 2B). This result is completely consistent withour data showing that mAb 806 becomes a “pan” EGFR antibody once thereceptor is denatured by SDS-PAGE (27).

Binding of mAb 806 to an EGFR Peptide Containing the Putative Epitope

A peptide (₂₈₇CGADSYEMEEDGVRKC₃₀₂) corresponding to a cysteine looplikely to contain the putative mAb 806 epitope was synthesized. Thispeptide was able to inhibit the binding of mAb 806 to the 1-501 and274-501 EGFR fragments in an immunoblot. (FIG. 3A, upper panels). Thepresence of EGFR fragments on both portions of the immunoblot wasconfirmed by stripping and re-probing with anti-myc (FIG. 3A, lowerpanel). The 287-302 EGFR peptide in solution was also able to inhibitthe binding of mAb 806 to the immobilized 1-501 fragment using an ELISAformat (FIG. 3B). Interestingly a shorter peptide (amino acids 287-298)did not inhibit the binding of mAb 806 at the concentrations tested(FIG. 3B). Thus, the mAb 806 epitope appears to be contained within theresidues 287-302, which form a disulfide-constrained loop in the EGFR.

We also tested the ability of the 287-302 EGFR peptide to inhibit thebinding of mAb 806 to immobilized 501-Fc, a dimeric version of the 1-501EGFR fragment fused to the Fc region of human IgG1. Oxidized, reducedand aged (i.e. moderately aggregated) peptide all inhibited binding ofmAb 806 to 501-Fc in a dose dependent manner (FIG. 4A). A peptidecontaining reduced and S-carboxymethylated cysteine residues was unableto inhibit the binding of mAb 806 indicating that one or both cysteineresidues contribute to the mAb 806 epitope (FIG. 4B). N-terminal(CGADSYEM) (SEQ ID NO: 16) or C-terminal (EEGVRKC) (SEQ ID NO: 17)peptide fragments generated by cyanogen bromide cleavage were incapableof inhibiting mAb 806 binding (FIG. 4B), implying that the epitope spansthe internal methionine residue. This data provides further confirmationthat the mAb 806 epitope is contained within the EGFR-derived peptide287-302.

The 287-302 EGFR peptide was coupled to a CM5 sensor chip bythiol-disulphide exchange coupling at a terminal cysteine residue andmAb 806 binding analyzed by surface plasmon resonance (BIAcore). The mAb806 bound the immobilized peptide in a dose dependent manner (FIG. 5A)with an apparent affinity of 30 nM (FIG. 5A), which is consistent withthe affinity obtained using Scatchard analysis on live cells (27). Mab806 binding to a blank channel, a cysteine-blocked channel or anirrelevant peptide were all less than 1% of the binding to the 287-302EGFR peptide (data not shown). Since the affinity of mAb 806 for thispeptide is similar to the affinity displayed for de2-7 EGFR it appearsthat the peptide contains all the major determinants that contribute tothe epitope. As the peptide was immobilized using thiol-coupling andtherefore cannot form an intramolecular disulfide bond, this observationfurther demonstrates that the loop does not have to cyclized for mAb 806binding. We also immobilized the 287-302 EGFR peptide via amine couplingand showed that mAb 806 still bound (FIG. 5B).

We then tested the ability of several EGFR peptides in solution to blockbinding of mAb 806 to immobilized 287-302 EGFR peptide. As expected thesoluble 287-302 EGFR peptide inhibited mAb 806 binding in a dosedependent manner (FIG. 5B, upper panel). Consistent with our ELISA data(FIG. 3B) the 287-298 EGFR peptide was unable to prevent binding of mAb806 even when used in vast excess (FIG. 5B, middle panel). An additionalpeptide, simply lacking C302 (i.e. amino acids 287-301) was able toweakly inhibit mAb 806 binding in a dose dependent manner (FIG. 5B,lower panel). These observation confirm that the amino acid residue C302is required for high affinity mAb 806 binding.

Structural Analysis of the mAb 806 Epitope and its Relationship to EGFRActivation

Several recent crystallographic studies have described the structure ofthe EGFR extracellular domain. Thus, we analysed the mAb 806 epitope interms of its structural location to determine if this could help explainits unique specificity. The cysteine-loop containing the mAb 806 epitope(FIG. 6A) is located at the C-terminal portion of the cysteine richCR1-domain (FIG. 6B, magenta). Interestingly, this region of the EGFR isone of the most poorly characterized in the structure suggesting arelatively degree of flexibility. A considerable portion of the 287-302EGFR loop is buried within the EGFR, however two regions are moreexposed and are potentially accessible by antibody. The first of theseis centred on D290 (FIG. 6C, highlighted in magenta in the left-sideview) and the second of these is focused on D297, which can be observedwhen the molecule is rotated 180° (FIG. 6C, highlighted in magenta inthe right-side view).

The tethered form of the EGFR depicted in FIG. 6C is an inactiveconformation of the receptor. In this state the EGFR CR2-domaininteracts with the CR1-domain in a manner that prevents the dimerizationarm, a small loop contained within the CR1-domain, from interacting withthe dimerization arm of other EGFR molecules. Untethering of the EGFRleads to an extended-form of the receptor in which the dimerization armis exposed (FIG. 6D, left panel) allowing the receptor dimerization tooccur (FIG. 6B). Our current understanding suggests that when inequilibrium on the cell surface 95% of the EGFR is in the tetheredconformation (37). The remaining EGFR would be in the active dimer orextended untethered conformation. Addition of ligand would drive more ofthe receptor into the dimeric form (FIG. 6B).

With respect to possible mAb 806 binding sites the only residuesaccessible in the tethered form of the receptor are those centred onD297. However, given that mAb 806 only binds 5-10% of EGFR in cell linesover-expressing the receptor, it is extremely unlikely mAb 806 binds tothe tethered form of EGFR, which forms 95% of EGFR on the cell surface.Based on the structural information presented in FIG. 6, dimerization ofthe EGFR does not expose any additional amino acid residues within themAb 806 epitope and therefore would not be a target for mAb 806 binding.Given the size of an antibody, none of the exposed amino acids centredon D290 would be accessible to the mAb 806 in either the tethered ordimeric conformation. As the EGFR moves from the tethered conformationto the active dimeric state it must pass through a transitional extendedstate. This transitional form of the EGFR (FIG. 6D) may be monomeric, orpossibly an inactive dimer, and would be comparatively rare on the cellsurface consistent with the level of mAb m806 binding. Significantly, inthis transitional form of the receptor the residues around D290 as wellas a number of amino acids normally buried (e.g. Y292 and M294) would beaccessible to antibody binding. Spatial considerations would stronglyindicate that binding of mAb 806 to the region near D290 would requireinteraction with amino acids outside the cysteine loop, a possibilityinconsistent with our affinity data that suggests the entire mAb 806epitope is contained within the cysteine loop. If we eliminate D290 as abinding region, then mAb 806 must interact with the region aroundY292/M294 although the epitope may extend further to include D297. Takentogether, the only consistent conclusion is that mAb 806 binds to aminoacids only exposed in the extended form of the EGFR before it undergoesdimerization.

Binding of mAb 806 to Constitutively Untethered Forms of the EGFR

In order to confirm that mAb 806 preferentially binds thenon-dimerized/untethered EGFR we stably expressed a mutation of the EGFRlacking the CR1 dimerization arm (deCR1-loop) in 293 cells (31). Thisregion was chosen due to its role in forming active EGFR dimers andbecause the CR1 dimerization arm is also integrally involved in theCR1:CR2 interactions associated with tethering. Thus, the deCR1, likethe de2-7 EGFR should be constitutively untethered. The parental 293cells express a low level of wild type EGFR (approximately 1×10⁴EGFR/cell) as evident by the binding of mAb 528 by FACS (FIG. 7). Asexpected, mAb 806 does not bind the endogenous EGFR expressed in thesecells. The de2-7 EGFR, like the deCR1-loop, should not be able to tetherand should have reduced dimerization. Transfection of 293 cells with thede2-7 EGFR led to robust binding of mAb 806 as previously shown in othercell lines (FIG. 7). Binding of the highly conformational dependant mAb528 to the deCR1-loop EGFR confirms that there is no gross change to itsconformation (FIG. 7). Indeed, we have previously shown that thedeCR1-loop EGFR can bind ligand further supporting the notion that itsoverall structure remains intact (31). Flow cytometry analysis of twoindependent deCR1-loop EGFR expressing clones, clearly showed binding ofmAb 806 (FIG. 7). Thus, consistent with our hypothesis, mAb 806 appearsto bind to the transitional untethered EGFR before it forms an activedimer. MAb 806 also shows increased binding to EGFR point mutants thathave a reduced capacity to tether (see EXAMPLE 2 below)

Discussion

The mAb 806 was generated following immunization with mouse fibroblastsexpressing the de2-7 EGFR and was selected by mixed hemadsorption assayfor high reactivity to de2-7 EGFR and negligible activity against thewild type EGFR (21). Further characterization soon revealed that mAb 806could recognize cell lines and glioma specimens when the wild type EGFRwas over-expressed, especially when the EGFR gene was amplified, but notnormal tissue (21). Recently, we demonstrated that mAb 806preferentially binds the high-mannose form of both the de2-7 and wildtype EGFR located within the endoplasmic reticulum. Furthermore, wedemonstrated that some of the high-mannose wt EGFR is misdirected to thecell surface when cells over-express the receptor. This work however,did not identify the mAb 806 epitope or adequately explain the robustanti-tumor activity mediated by mAb 806. Using two independentmethodologies we identified a cysteine loop (amino acids 287-302) thatcontains the mAb 806 epitope. Since the mAb 806 affinity to a syntheticpeptide encompassing residues 287-302 is similar to what we havepreviously measured by Scatchard analysis with de2-7 EGFR expressingcell lines (27), we are confident it contains the complete epitopesequence. Clearly, the peptide does not have to be restrained in adisulfide-bonded loop for antibody binding since mAb 806 recognizedreduced peptide in solution, thiol-immobilized peptide and weakly bounda soluble peptide with C302 deleted.

Both immunoprecipitation and Scatchard analysis demonstrated that mAb806 recognizes between 5-10% of the wild type EGFR expressed on thesurface of A431 cells (27), a cell line over-expressing the receptor dueto an amplification of the EGFR gene. Despite binding a low proportionof receptors, mAb 806 displays robust anti-tumor activity against A431xenografts grown in nude mice (22, 23). Our observation that mAb 806preferentially binds the untethered EGFR suggests a probable mechanismfor this anti-tumor activity. As an EGFR molecule untethers, it enters atransitional state between inactive tether and active dimmer (37). It isthis transitional untethered form of the EGFR that is engaged by mAb806. Binding of mAb 806 then prevents the formation of signaling-capableEGFR dimers (FIG. 8). Thus, while mAb 806 only binds a low percentage ofthe EGFR at any given instant, over an extended period of time it wouldbe capable of inhibiting a substantial proportion of EGFR signalingwhich in turn generates an anti-tumor effect in vivo. The fate of themAb 806 bound EGFR is unknown, although we have previously shown thatthe mAb 806/de2-7 EGFR complex is internalized (27). Alternately, themAb806/EGFR could remain trapped on the surface in an inactive form, asis the case following treatment of cells with small molecule weighttyrosine kinase inhibitors specific to the EGFR (28, 38). In contrast tothe wild type EGFR, mAb 806 recognizes approximately half of the de2-7EGFR molecules expressed on the cell surface when compared to DH8.3(27), an antibody specific for the mutant receptor. The increasedreactivity of mAb 806 for the de2-7 EGFR is consistent with the factthat this mutant receptor lacks the CR1-dimerization loop and thereforecannot assume the tethered conformation.

If mAb 806 recognizes a normal, but comparatively low abundant,transitional conformation of the EGFR why does it fail to bind normaltissues or cell lines expressing “average” levels of EGFR? Thisobservation appears unrelated to sensitivity of detection, as in aprevious study we showed that iodinated mAb 806 did not bind to a U87MGglioma (1×10⁵ EGFR/cell) cell pellet containing 1×10⁷ cells, which basedsmaller A431 cell pellet should have been sensitive enough to measurelow level binding. We have determined that glycosylation influences mAb806 reactivity and that mAb 806 preferentially recognizes thehigh-mannose form of the EGFR that normally resides within theendoplasmic reticulum. Furthermore, in cells over-expressing the EGFRsome of this high-mannose receptor is misdirected to the cell surface.

Even though the sequence homology of the mAb 806 epitope is relativelylow in ErbB3/B4, the size and location of the cysteine loop isconserved. Furthermore, there are two amino acid residues completelyconserved (E293 and G298) and a further two where charge is conserved(E295 and R300). Finally, the overall structure of ErbB3 (and probablyErbB4), is very similar to that of the EGFR in that it adopts a tetheredconformation that presumably untethers during activation (41). Takentogether this suggests that antibodies targeted to the equivalentcysteine loop in ErbB3/B4 have similar properties to mAb 806 (i.e.specificity restricted to tumors and the ability to block receptoractivation). More broadly, our data suggests that the generation ofantibodies to transitional forms of growth factor receptors represents anovel way of reducing normal tissue targeting yet retaininganti-signaling activity. Accordingly, comparisons between the structureof active (ligand bound) receptors and their inactive counterpartsshould identify amino acids transiently exposed during receptorconformational changes. Finally, mAb 806 was generated by immunizingwith cells expressing a constitutively active mutation of the EGFR andselecting for antibodies specific to this mutated receptor. Thus,immunization with constitutively active receptor may provide ageneralized strategy that increases the likelihood of identifyingantibodies recognizing transitional forms of the receptor.

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Example 2 Analysis of CR1/CR2 Domain Interactions on the Function of theCell-Surface Epidermal Growth Factor Receptor

Recent crystallographic data on the isolated extracellular domain of theEpidermal Growth Factor Receptor (EGFR) have suggested a model for itsactivation by ligand. We have tested this model in the context of thefull-length EGFR displayed at the cell surface, by introducing mutationsin two regions (CR1 and CR2) of the extracellular domain thought to becritical for regulation of receptor activation. Mutations in the CR1 andCR2 domains have opposing effects on ligand binding affinity, receptordimerization, tyrosine kinase activation and signaling competence.Tyr²⁴⁶ is a critical residue in the CR1-loop, which is implicated in thepositioning and stabilization of the receptor dimer interface afterligand binding: mutations of Tyr²⁴⁶ impair or abolish receptor function.Mutations in CR2, which weaken the interaction that restricts thereceptor to the tethered state, enhance responsiveness to EGF byincreasing affinity for the ligand. However, weakening of the CR1/CR2interaction does not result in spontaneous activation of the receptors'kinase. We have used an antibody (mAb806), which recognizes a transitionstate of the EGF receptor between the negatively constrained, tetheredstate and the fully active back-to-back dimer conformation, to followconformational changes in the wild-type and mutant EGF receptors afterligand binding. Our results suggest that EGFR on cell surface can beuntethered but this form is inactive; thus untethering of the receptoris not sufficient for activation, and ligand binding is essential forthe correct positioning of the two receptor subunits to achieve kinaseactivation.

Introduction

Over the last twenty years, the EGF receptor has provided importantopportunities for studying ligand activation of receptor-associatedintracellular tyrosine kinases (1-3). Recently, the three dimensionalstructures of the extracellular domains (ECDs) for several EGF receptorfamily members (EGFR, ErbB-2 and ErbB-3) have been reported (4-9). Thesestructures revealed two significantly different conformations for theEGF receptor ECD (4; 5; 9). In the crystal structure of the soluble,truncated ECD of the EGFR complexed with TGF-α (4) or with EGF (5) theligand is sandwiched between the L1 and L2 (ligand binding) domains, theECDs form back-to-back dimers, primarily through the two interlocked CR1(cysteine rich) domains; in contrast, in the crystal structure of theautoinhibited-EGFR in complex with EGF the ligand is bound only to theL1 domain, no dimer is present and the main intramolecular interactionof the monomeric receptor occurs between the CR1-loop and CR2 domain(9). In this structure, not only is the distance between L1 and L2 toogreat to allow simultaneous binding to one EGF molecule, but L2 is alsorotated away from the L1-bound EGF. Thus two critical featuresdistinguish the autoinhibited (tethered) from the untethered form of theEGF receptor ECD: the absence of dimers and the inability to bind ligandwith high affinity. Interestingly, the conformation of the truncated (8)and full-length (7) ErbB-2 ECD resembles the back-to-back EGFR dimer (4)whilst ErbB-3 ECD in the absence of ligand (6) has the same conformationas the tethered EGFR-ECD (9).

Work with the full length, cellular EGFR has established a strong linkbetween EGFR dimerization, high affinity binding and receptor kinaseactivation; whilst the crystal structures of the isolated ECDs providean improved framework for the understanding of these observations (i.e.ligand will bind with higher affinity to the “untethered” form of thereceptor, thus shifting the equilibrium away from the monomeric,autoinhibited receptor and favoring the formation of active dimers (9)),in the cellular environment the kinase and transmembrane domains of theEGFR also contribute to dimerization. Indeed cell-surface dimers (oroligomers) can be detected in the absence of ligand, although theunligated dimers do not have tyrosine kinase activity (10-16). Thus inthe full-length, cell-surface EGF receptor, ligand binding is requirednot only to drive dimerization, but for the formation of the kinaseactive conformation.

The structure and ligand binding properties of fragments or evenfull-length EGF receptor ECDs cannot unravel the complexity of signalingfrom cell surface displayed receptors. In this report, in order toimprove our understanding of the CR1-CR2 interactions on the processeswhich determine ligand binding, receptor conformational changes,receptor oligomerization and the regulation of kinase activity, we haveexpressed full-length EGF receptor mutants in intact mammalian (Baf/3)cells (17; 18). BaF/3 cells neither express endogenous EGF receptors,nor detectable levels of ligands which can perturb and/or activaterecombinant (mutant) receptors. The availability of the CR1-loop and CR2EGFR mutants and of the conformation-specific antibodies mAb528 (19) andmAb806 (20-23) have allowed us to probe the determinants of tetheringand to detect a major conformational transition when ligand binds to thereceptor.

Experimental Procedures

Reagents

Antibodies to the EGFR mAb528 (19) and mAb806 (20; 21) were produced andpurified in the GMP facility at the Ludwig Institute for CancerResearch, Melbourne. Anti-flag antibody M2 was purchased fromSigma-Aldrich, anti-phosphotyrosine (clone 4G10) and anti-EGFR (sheeppolyclonal) from Upstate (Lake Placid, N.Y.); anti-phospho-p44/p42 MAPKantibodies and anti-MAPK antibodies were purchased from Cell Signaling(Beverly, Mass.). HRP-coupled rabbit anti-mouse Ig and HRP-coupledrabbit anti-sheep Ig were obtained from BioRad (Hercules, Calif.) andDako (Fort Collins, Colo.) respectively. Alexa 488-labelled anti-mouseImmunoglobulin was purchased from Molecular Probes, Eugene, Oreg.PhenylArsine Oxide (PAO) was purchased from Sigma-Aldrich. The watersoluble, homobifunctional cross-linking reagents BS³ (spacer arm length:11.4 Å) and Sulpho-EGS (spacer arm length: 16.1 Å) were obtained fromPierce (Rockford, Ill.).

Generation of EGFR Mutant Constructs

Single point mutations of the wild-type EGFR were generated using asite-directed mutagenesis kit (Stratagene, La Jolla, Calif.). Thetemplate for each mutagenesis was the human EGFR cDNA; (24)) containingthe leader sequence followed by a FLAG tag coding sequence, in themammalian expression vector pcDNA3 (Invitrogen, Carlsbad, Calif.) asdescribed in (4). The automated nucleotide sequencing of each constructwas performed to confirm the integrity of each EGF receptor mutation.EGFR expression constructs were transiently expressed in 293 cells(American Type Culture Collection, Manassas, Va.) and the presence ofreceptor protein determined by staining with 528 and M2 antibodies toconfirm expression at the cell surface and to ensure protein foldingoccurred appropriately (data not shown).

Transfection of EGFR Constructs and Generation of Stable Cell Lines.

Wild-type and mutant EGFRs constructs were transfected into theIL-3-dependent murine hemopoietic cell line BaF/3 as describedpreviously (25). Transfected cells were selected in G418 for 10 days.Viable cells were screened for EGFR expression by FACS analysis on aFACStar (Beckton and Dickinson, Franklin Lakes, N.J.) using antibodiesto the flag tag (M2: 10 μg/ml in PBS/5% FCS/5 mMEDTA) and/or to the EGFRextracellular domain (mAb528: 10 μg/ml in PBS/5% FCS/5 mMEDTA) followedby Alexa 488-labelled anti-mouse Ig (1:400 final dilution). Backgroundfluorescence was determined by incubating the cells with an irrelevant,class matched primary antibody. Positive pools were sorted for theappropriate level of EGFR expression on a FACS-DIVA (Becton andDickinson). After final selection, mRNA was isolated from each cell lineand all mutations in the EGFR were confirmed by PCR annalysis. All cellswere routinely passaged in RPMI/10% FCS/10% WEHI3B conditioned medium(26) and 1.5 mg/ml G418.

Ligand Binding.

Murine EGF, purified from mouse submaxillary glands (27), was iodinatedusing Iodogen (28) to a specific activity of 5-8×10⁵ cpm/pmol. Ligandbinding to cells expressing the wt or mutant EGFR was determined at roomtemperature in the presence of the internalization inhibitorphenylarsine oxide (PAO) (29) by cold saturation experiments. Briefly,cells were incubated in PBS/1% BSA/30 μM PAO with or without increasingamounts of unlabelled EGF (20 pM-5.12 nM) and with a constant amount(300 pM) of ¹²⁵I EGF. Non-specific binding was determined using a500-fold excess of unlabelled EGF over ¹²⁵I-EGF. All experimental pointswere prepared in triplicate. At the end of the incubation, the cellswere pelleted and washed twice in ice-cold PBS before transferring tofresh tubes for counting in a Wallac WIZARD γ-counter (PerkinElmer,Boston, Mass.). Scatchard plots and estimates of ligand bindingaffinities and receptor numbers were obtained using the Radlig program(BioSoft, Cambridge, UK).

Receptor Cross Linking, Tyrosine Phosphorylation and MAPK Activation

BaF/3 cells expressing the wt or mutated EGFR were incubated in mediumwithout IL-3 and FCS for 3 hrs. Cells were collected by centrifugation,washed twice in PBS and incubated in PBS at room temperature with orwithout EGF (100 ng/ml) for 10 minutes. In cross-linking experiments thecells were incubated with 1.3 mM BS³ or Sulpho-EGS (PierceBiotechnologies, Rockford, Ill.) for 20 min at RT after PBS or EGFtreatment. Cells were lysed in SDS/PAGE sample buffer with or withoutreducing agent (100 mM β-mercapoethanol). Total cell lysates wereanalysed directly by SDS-PAGE on 3-8% Tris/Acetate or 4-12% Bis/Trisgradient gels (In Vitrogen, Carlsbad, Calif.) and transferred to PVDFmembranes before immunodetection with anti-phosphotyrosine antibodies(4G10, UBI, 1:1000 final dilution)), anti-EGFR antibodies (Sheepanti-EGFR, UBI, 1:1000 final dilution) or anti-phospho-MAPK antibodies(1:1000 final dilution) followed by HRP-coupled anti-mouse, anti-sheep,or anti-rabbit Ig respectively (all at 1:3000 final dilution). Reactivebands were visualized with ECL reagent (Amersham). To determine specifictyrosine phosphorylation of the EGFR, membranes probed withanti-phosphotyrosine antibodies were stripped with a solution of 0.1Mglycine (pH 2.1) and reprobed with anti-EGFR or anti-phospho MAPKantibodies. The films were scanned on a Molecular Dynamics scanningdensitometer (Molecular Dynamics, Sunnyvale, Calif.) and bandquantitation was performed in ImageQuant using wide-line peakintegration.

Mitogenic Responses to EGF

Cells growing in log-phase were harvested and washed three times toremove residual IL-3. Cells were resuspended in RPMI 1640+10% FCS andseeded into 96 well plates using the Biomek 2000 (Beckman) at 2×10⁴cells per 200 μl and incubated for 4 hours at 37° C. in 10% CO₂. EGF wasadded to the first titration point and titrated in duplicate as two-folddilutions across the 96 well plate. Control wells received WEHI-3Bconditioned medium at a final concentration of 5% (v/v). ³H-Thymidine(0.5 μCi/well) was added and the plates incubated for 20 hours at 37° C.in 5% CO₂, before being harvested onto nitrocellulose filter mats usingan automatic harvester (Tomtec, Conn., USA). The mats were dried in amicrowave, placed in a plastic counting bag and scintillant (10 ml)added. Incorporated ³H-Thymidine was determined using a beta counter(1205 Betaplate, Wallac, Finland).

Reactivity with Conformation-Specific Antibodies

Cells were preincubated with antibodies, EGF or control medium prior toantibody staining and FACS analysis. Preincubation with antibodies(mAb528, mAb806 or a class-matched irrelevant antibody, all at 10 μg/ml)was carried out at 37° C. in RPMI/10% FCS for times ranging from 30 minto 16 hrs. Preincubation with EGF (100 ng/ml in ice-cold FACS buffer)was carried out on ice for 20 min. After preincubation, cells werecollected by centrifugation and stained with the control or testantibodies (all at 10 μg/ml in FACS buffer for 20 min. on ice, washed inFACS buffer) followed by Alexa 488-anti mouse Ig (1:400 final dilution,20 min on ice) to detect the primary antibody. The cells were washedwith ice-cold FACS buffer, collected by centrifugation and analysed on aFACScan; peak fluorescence channel and median fluorescence weredetermined for each sample using the Statistical tool in CellQuest(Becton and Dickinson). Background (negative control) fluorescence wasdeducted from all measurements. The median fluorescence values werechosen as most representative of peak shape and fluorescence intensity,and were used to derive the ratio of mAb806 to mAb528 binding.

Results and Discussion

The aim of this work is to determine the role of CR1-loop/CR2interactions on the conformational preferences, mechanism of activationand signalling potential of the full-length, cell-surface expressedEGFR. We have introduced point mutations in the CR1 and CR2 domainswhich would be expected to perturb the CR1/CR1 and/or CR1/CR2interactions, and consequently alter the balance between the tethered,untethered, inactive and/or active states of the EGFR. These constructshave been expressed in BaF/3, a hemopoietic cell line which is devoid ofendogenous ErbB family members. We have analysed the effects of themutations on the function of the EGFR by determining binding kinetics,dimerization, ligand-dependent tyrosine phosphorylation and signalling,and the ability to induce DNA synthesis in an EGF-dependent manner.These parameters are however indirect measures of receptoroligomerization, configuration or conformational changes; therefore, wehave also used the binding of two conformationally specific anti-EGFRantibodies, mAb528 (19) and mAb806 (20; 23; 30), as a tool to assess theeffect of mutations on the “resting” conformation of the EGFR and on thedynamics of ligand-induced conformational and configurational changes.

Receptor Expression and Preliminary Characterization:

Six point mutations have been analysed in detail (see FIG. 9A, 9B):three CR1 mutations at Tyr²⁴⁶ (Phe, Trp and Asp) and three CR2substitutions at Asp⁵⁶³ (to His), Glu⁵⁷⁸ (to Cys) and Val⁵⁸³ (to Asp).In an attempt to disulphide link the CR1/CR2 interaction, we prepared amutant with a substitution in each of CR1 and CR2 (Leu²⁴⁵ to Cys andGlu⁵⁷⁸ to Cys). The recombinant EGFRs were expressed in the hemopoieticcell line BaF/3, which is ideal for the biochemical characterization ofthe EGFR (18; 25). After transfection and selection in G418, receptorexpression was monitored using the anti-flag antibody M2 as well as themonoclonal antibody 528, which is directed to the extracellular domainof the EGFR, blocks ligand binding (19) and is reported to recognizeonly the native form of the receptor. Based on the reactivity with theseantibodies, all mutant receptors appear to be correctly folded and areexpressed at the cell surface. After multiple rounds of FACS sorting weobtained cell lines expressing similar levels (20-40,000 R/cell) of themutant or wtEGFR (FIG. 10). It is essential that receptor expression isbelow 100,000 receptors/cell: transient expression experiments usuallyyield high levels of cell-surface EGFR (>10⁵/cell), however at theselevels of expression there often is spontaneous activation (ieligand-independent tyrosine phosphorylation) of the EGFR. The reasonsfor the activation are not clear, but may be due to oligomerization,incorrect processing or mis-folding of the receptor; we have sought toavoid this complication by producing cell lines expressing <50,000R/cell.

Ligand Binding by EGFR Mutants:

From the crystal structures of the tethered (9) and untethered (4; 5)ECD of the EGFR, it has been postulated that the affinity of the ligandfor the two form will be quite different. In the untethered conformationthe ligand can make contacts with both the L1 and L2 domains, while inthe tethered conformation the ligand can only bind the L1 or L2 domains.Ferguson et al (9) have reported that weakening the interaction betweenthe CR1 and CR2 loops increases the apparent affinity of the EGFR-ECDfor EGF; however the link between tethering of the CR1-loop and the CR2domain and ligand binding affinity is based on data obtained by BIAcoreanalysis of the isolated EGFR-ECD (9; 31). Kinetic binding data for fulllength EGFR at the cell surface yield affinity constants which are atleast two orders of magnitude lower, 20 pM-2 nM compared to 20-350 nMfor the EGFR-ECD. The binding kinetics of EGFR to its ligands in acellular context are complicated by structure-independent factors suchas local receptor density, oligomerization state, and interactions withcytosolic or cytoskeletal elements (32-34). In the context of the fulllength receptor, modifications in the kinase, transmembrane and/orC-terminal domains also influence the affinity of the EGFR for itsligands (35-39). Therefore it is important to measure the effects of CR1and CR2 mutations on the ligand binding affinity, oligomerization stateand signalling (see later) of the receptor in intact cells. To preventinternalization while assessing ligand binding at a physiologicaltemperature, affinity determinations were carried out in the presence of30 μM Phenylarsine oxide (29): under these assay conditions,internalization of the EGFR was reduced to >1% (data not shown) Theresults of Scatchard analyses of EGF binding to wt and mutant EGFR arepresented in TABLE 3 and FIG. 11 and are summarized below.

TABLE 3 Scatchard analysis of ¹²⁵I-EGF binding to BaF/3 cells expressingwt or mutant EGF receptors. Cell line K_(d)1 (pM) % of sites K_(d)2 (nM)% of sites R/cell × 10^(−4(a)) wt-EGFR   29 +/− 9    2.6 +/− 0.4  1.6+/− 0.6     97.5 +/− 0.49 3.4 +/− 0.7 CR1-loop mutants: Y²⁴⁶F — — 2.8+/− 0.9 (100) 3.0 +/− 0.2 Y²⁴⁶W — — 2.5 +/− 0.05 (100) 2.9 +/− 0.2 Y²⁴⁶D— — 2.1 +/− 0.3 (100) 1.2 +/− 0.1 CR2-loop mutants: V⁵⁸³D    2.6 +/−1.3   12.6 +/− 4  1.3 +/− 0.3    90.8 +/− 1.9  3.8 +/− 0.71 D⁵⁶³H   17.6+/− 4.4   4.4 +/− 0.7) 1.7 +/− 0.8    96.4 +/− 0.7 2.3 +/− 0.8 E⁵⁷⁸C — —1.7 +/− 0.6 100 3.45 +/− 0.12 L²⁴⁵C/E⁵⁷⁸C — — 2.1 +/− 0.3 100   0.37 +/−0.002^(b) ¹²⁵I-EGF binding was performed as described in “Materials andMethods”. Data were analyzed using the “Kell for Windows” RadLigprogram. ^((a))Number of receptors per cell were calculated from theB_(max) and the number of cells/tube in each ligand binding experiment.Results are the average and standard error of at least three separateexperiments. ^(b)Receptor number determined by Scatchard analysis(B_(max)) was less than 10% of the receptor number estimated by FACS orby immunoblotting

CR2 mutations: the V⁵⁸³D and D⁵⁶³H mutations were designed to disruptthe CR2/CR1-loop interactions. In the tethered conformation the γ-methylgroups of the V⁵⁸⁷ side-chain are in close van der Waals contact withY²⁴⁶: substituting the Asp γ-carboxyl should disrupt the CR1/CR2interface. Similarly, the γ-carboxyl of D⁵⁶³ is hydrogen bonded to Y²⁴⁶in the tethered conformation, and substitution of the aspartate carboxylgroups with the imidazole of His will weaken the interaction. In cellsexpressing V⁵⁸³D there is a significant increase in the proportion ofhigh affinity EGF binding sites compared to cells expressing the wtEGFR(12.6% vs 2.6%, respectively). This trend is also observed in the D⁵⁶³Hmutant, although in this case the difference from wt was notstatistically significant (TABLE 3). An increase in the proportion ofhigh affinity sites is an indication of a shift in the equilibriumtowards the untethered states of the receptors, supporting theassumption that V⁵⁸³D and D⁵⁶³H mutations weaken the CR1/CR2interactions. In order to investigate the possibility of creating adisulphide bond to covalently link CR1 and CR2, we identified tworesidues which have appropriate distance and side-chain orientation inthe tethered conformation: Leu²⁴⁵ and Glu⁵⁷⁸. Initially we made thesingle mutation E⁵⁷⁸C and then the double mutation L²⁴⁵C/E⁵⁷⁸C.Interestingly, the E⁵⁷⁸ side-chain is close to the side-chains of bothL²⁴⁵ and P²⁴⁸, so the E⁵⁷⁸C substitution might be expected to improvethe packing of the CR1-loop/CR2 interface by increasing hydrophobicinteractions with these residues. Experimentally, the E⁵⁷⁸C mutationcompletely abolishes high-affinity EGF binding without affecting thenumber of low affinity sites (TABLE 3). The introduction of a cysteinein this position does not appear to affect the folding of either or bothcysteine-rich domains: the conformation dependent antibody mAb528 bindsto the mutant receptor, and its phosphorylation and signalling arestill-dependent on EGF (see later).

CR1-loop mutations: we introduced three different amino acidsubstitutions (Phe, Trp and Asp) for Tyr²⁴⁶. The crystal structuresuggests Y²⁴⁶ is critical for both the CR1/CR1 and CR1/CR2 interactions(FIG. 9B,9C). In the tethered configuration the CR1-loop interactsclosely with the CR2 domain; Tyr²⁴⁶ hydrogen bonds with the carboxylside-chain of Asp⁵⁶³. Asp⁵⁶³ is held in place by a small bridge with theε-amino of Lys⁵⁸⁵. Mutation of Tyr²⁴⁶ to Phe removes the H-bond so thetether will be weaker. The Trp²⁴⁶ mutant is too large to fit into theCR2 binding site, and indeed it would disrupt the Lys⁵⁸⁵-Asp⁵⁶³ saltbridge. Replacing Tyr²⁴⁶ with Asp will lead to the loss of hydrophobicpacking as well as to a strong repulsion between Asp²⁴⁶ and Asp⁵⁶³. Thusall mutations should render the tethered conformation less favorable. Toactivate the EGFR kinase, the back-to-back dimer must form, so that thehydroxyl of Tyr²⁴⁶ hydrogen bonds to the opposing chain (FIG. 9).Indeed, in the presence of ligand, the hydroxyl is H-bonded to thebackbone at residues Ser²⁶², Gly²⁶⁴ and C²⁸³. These three hydrogen bondswill be missing in the Phe²⁴⁶ and Asp²⁴⁶ mutants. The packing betweenTyr²⁴⁶ and the opposing chain is tight, with no room for a Trp residue:it is expected that the Trp²⁴⁶ dimer would not be closely packed.Experimentally, all three mutations resulted in loss of high affinityEGF binding (TABLE 3 and FIG. 11), suggesting a severe impairment of theCR1/CR1 interaction which is not compensated by the untethering ofCR1/CR2 binding.

Taken together, these observations confirm that ligand binding to the“tethered” form of the EGFR occurs with low affinity; low affinity EGFbinding appears to be independent of the relative positioning of L1 andL2 domains. Inspection of the crystal structure indicates that theligand binding surfaces of both domains are available in both thetethered and untethered conformations, so low affinity bindingpresumably reflects binding to either site, or to both sitesindependently. Clearly, untethering can increase the proportion ofreceptors available for high affinity binding. It is interesting to notethat the high affinity conformation requires the CR1 loop, presumably byinfluencing the juxtaposition of L1 and L2 in the dimeric complex.

Receptor dimerization: EGF binding to the extracellular domain of thereceptor leads to the formation or stabilization of kinase-active EGFR.The ligand-induced CR1/CR1 interaction is necessary for the formation ofan active EGFR complex: deletion of the CR1 loop abolishes the abilityof the EGFR-ECD to dimerize, even in the context of a the full lengthEGFR (4). Clearly, mutations in the CR1 and CR2 loops have significanteffects on EGF binding affinity (FIG. 11 and TABLE 3): we wereinterested to determine the effect of these mutations on basal andligand-mediated dimerization and kinase activation. Cells were treatedwith EGF and the homobifunctional, cell-impermeable cross-linker BS³ for30 min. at room temperature. Cell lysates were separated by SDS-PAGE andimmunoblotted with either anti-EGFR or anti-phosphotyrosine antibodies.The results are shown in FIG. 4 and summarized below.

CR1-loop mutants had reduced ligand dependent dimerization; inparticular the Y²⁴⁶D mutation completely abolished ligand-dependentdimerization. However, basal dimerization was only marginally affected:this points to a different role of the conformation of Y²⁴⁶ in thespontaneous and ligand-mediated dimerization interface. Given thecomplete lack of detectable dimers in the Δ-CR1-loop receptor, in whichthe whole of the CR1-loop is deleted (4), it is possible that otherregions in this loop contribute to the formation of the unligated dimer.The phosphotyrosine content of both the monomeric and dimeric Y²⁴⁶mutant receptors was also reduced, suggesting that, even when dimers doform, the ECD conformation does not permit kinase activation: eventhough some spontaneous dimers could be detected in the Y²⁴⁶W mutant, inthe absence of ligand there is virtually no phosphorylation of thedimer. Clearly, the formation of ECD-crosslinkable dimer is reduced inall the Y²⁴⁶ mutants. It is interesting to note that the phosphotyrosinecontent of the Y²⁴⁶ mutant monomers after EGF stimulation isparticularly affected (FIG. 12C); since the monomers presumably aregenerated from dimers which have failed to cross-link, they may reflecta sub-population of molecules with altered (weaker) interactions in thedimeric complex. Whether the Y²⁴⁶ mutations overall affect the stabilityof the dimer, prevent a re-orientation of the dimer subunits or theformation of higher order oligomers necessary for kinase activation,cannot be addressed directly in our experimental system.

CR2 mutants had normal levels of basal and ligand-dependentdimerization. We did not detect significant increases in the proportionof dimers for mutant EGFR in which the CR1/CR2 tether had been weakened,suggesting that, even when the mutations lead to untethering, theformation of the BS³-crosslinkable dimeric complex is dependent on thebinding of ligand. The mutation of E⁵⁷⁸ to C introduces an unpairedcysteine and could conceivably lead to the formation of adisulphide-bonded dimer. We have investigated this possibility usingcross-linkers of different spacer-arm length (BS³, 11.3 Å andSulpho-EGS, 16.1 Å), as well as analysing non-cross-linked dimers underreducing and native conditions (data not shown): we found no evidence ofspontaneous dimerization of the E⁵⁷⁸C mutant and conclude that Cys⁵⁷⁸does not lead to the formation of interchain disulphide bonds.

Ligand-dependent tyrosine phosphorylation and MAPK signalling:CR1-loop/CR2 interactions appear to stabilize a kinase-inactiveconformation of the EGFR and prevent spontaneous activation (9). Wemonitored basal and EGF-dependent tyrosine phosphorylation, as well asMAPK activation, in cells expressing the mutant receptors. The resultsare presented in FIG. 13. Ligand binding causes some increase in thephosphotyrosine content of most mutant receptor molecules; however thespecific activation of individual mutants (measured by the ratio oftyrosine phosphorylation to receptor protein and by specific activationof MAPK: FIG. 13B,13C) varied significantly. All CR2 mutants areactivated by ligand at levels similar to the wt receptor. Even E⁵⁷⁸C,which has only low affinity sites and hence should occur predominantlyin the tethered (inactive) form, can be fully stimulated at highconcentrations of EGF (16 nM). We tested the correlation between ligandbinding affinity and signalling of the CR2-mutant receptors by exposingthe cells to increasing concentrations of EGF (30 pM to 100 nM) andmonitoring the induction of tyrosine phosphorylation and MAPK activation(FIG. 14). In E⁵⁷⁸C-EGFR expressing cells, peak phosphorylation of theEGFR and the signal transducers Shc and MAPK was only achieved atsignificantly higher concentrations of EGF compared to the wt. Incontrast, activation of the receptor for the V⁵⁸³D and D563H-EGFRexpressing cells occurred at lower concentrations of EGF then wtEGFR(FIG. 14B,14C). These results support the concept that mutations in theCR2 domain affect binding affinity but not the subsequent events whichtrigger receptor function. Even at saturating amounts of EGF, all Tyr²⁴⁶mutants have severely reduced receptor tyrosine phosphorylation and MAPKactivation (FIG. 13): the ability to form a productive CR1/CR1 loopinteraction is critical for kinase activation. Other point mutations tothe CR1 loop or its docking regions (Y²⁵¹A, F²⁶³A) appear to have hadminimal effects on EGFR signalling (5). However when both the CR1 loopand its docking site are disrupted (eg Y²⁵¹A/R²⁸⁵S double mutant: (5)),signalling is disrupted completely. These authors also reported areduction in the level of ligand binding, suggesting engagement of thedimerization docking site may influence the ability of L1 and L2 domainsto re-orient in response to EGF.

Mitogenic signalling from EGFR mutants. Ultimately, the functionality ofEGFR is measured by its ability to stimulate biological responses. Theseresponses depend on a host of parameters, including affinity of ligandbinding, strength of kinase activation, magnitude of the kinaseactivation, duration of signalling. We have tested the EGFR mutants fortheir ability to induce “de novo” DNA synthesis following exposure toincreasing concentrations of EGF, using a [³H]Thymidine incorporationassay. The results are presented in FIG. 15 and TABLE 4. Firstly, noneof the cell lines exhibited ligand-independent [³H]thymidineincorporation: it is clear that even when the tether between the CR1loop and CR2 has been weakened, mitogenic signalling requires EGFbinding for the activation of the receptor. Although generally the EC₅₀for EGF correlate well with the high affinity receptor occupancy (cf.TABLE 3 and TABLE 4), in the case of E⁵⁷⁸C there is a 10-fold differencebetween the concentration of EGF required for half-maximal [³H]Thymidineincorporation and for half-maximal occupancy of the receptors. We haveestablished that, in the BaF/3 cell lines expressing wtEGFR, as few as500 R/cell need to be activated to achieve a half-maximal response toEGF (see Walker et al. 1998, for methodology); this threshold is reachedfor wtEGFR at ˜15 pM and for the E⁵⁷⁸C cells at ˜80 pM EGF (TABLE 4).Using the same calculations (based on the total number of receptors/celland the fractional occupancy at each EGF concentration) we haveestimated that the Y²⁴⁶W mutant should reach half-maximal response at anEGF concentration of ˜60 pM, and the Y²⁴⁶D mutant at a concentration of˜400 pM. The complete lack of response to EGF of these mutants in themitogenic assay reflects an inability of these EGFRs to form aproductive signalling unit rather than a simple loss of ligand bindingaffinity.

TABLE 4 Mitogenic response to EGF in wt and mutant EGFR [EGF] at whichEC₅₀ for 500R/cell % maximal EGF ^((b)) are occupied ^((c)) Cell Lineincorporation ^((a)) (pM) (pM) wt-EGFR 100 12 16 CR1 mutants: Y²⁴⁶F 1630 30 Y²⁴⁶W 0 — 60 Y²⁴⁶D 0 — 400 CR2 mutants: V⁵⁸³D 100 6 <1 D⁵⁶³H 90 58 E⁵⁷⁸C 100 100 80 BaF/3 cells expressing wt or mutant EGFR were exposedto increasing concentrations of EGF (0-10 ng/ml, 0-1.7 nM) and DNAsynthesis measured by [³H]Thymidine incorporation as detailed inExperimental Procedures. ^((a)) The response of wtEGFR-BaF/3 cells at 1nM EGF was taken as maximal. ^((b)) EC₅₀ was determined from thedose-response curves as shown in FIG. 7. ^((c)) The concentration of EGFneeded to occupy 500R/cells was calculated from the K_(d) and B_(max)data obtained by Scatchard analysis, using a plot of receptor occupancyvs EGF concentration. The number of EGFR occupied at each concentrationof EGF was calculated from the formula ([L]/[L] + K_(d1)) × R₁ +([L]/[L] + K_(d2)) × R₂ where [L] = EGF concentration; K_(d1) and K_(d2)= equilibrium binding constants; R₁ and R₂ = number of high- andlow-affinity receptors. The data are representative of at least threeseparate experiments

Antibody monitoring of EGFR conformations. The results presented so farsupport a model where interactions between the CR1 loop and the CR2domain constrain the EGFR to a low-affinity, kinase inactive state (9),and the CR1/CR1 loops interaction is necessary for ligand induced kinaseactivation of the EGFR (4; 5). It is still unclear whether an“intermediate” state also exists (as suggested by Ferguson et al., (9)),and what its properties may be. We would expect this form of thereceptor to be untethered, higher-affinity, dimeric and kinase inactive.In the absence of ligand, the correct CR1-CR1 interactions would beunlikely to form, or would be too transient to effect kinase activation.

Monoclonal antibody 528 (19) has been used as a competitive antibody forEGF binding to the human EGF receptor. Although the exact epitope formAb528 has yet to be mapped, mAb528 reacts with the Δ2-7 EGFR (whichlacks L1 and most of CR1 domains: (40)) and interferes with ligandbinding to the wtEGFR, so we presume that the epitope resides on the L2domain. The antibody is specific for the human EGFR and recognizes onlythe correctly folded receptor (i.e. it does not react with the reducedform of hEGFR in Western Blots). Reactivity of all the mutants used inthis study with mAb528 is unimpaired, and receptor numbers determined byFACS analysis using mAb528 or Scatchard analysis using ¹²⁵I-EGF areusually in agreement. As mentioned earlier the L²⁴⁵C/E⁵⁷⁸C mutant,whilst fully reactive with mAb528, has only 10% of the expected numberof low affinity EGF binding sites.

Monoclonal antibody 806 recognizes the Δ2-7 truncated EGFR as well as asubpopulation of wtEGFR in cells overexpressing the receptor (23; 30)mAb806 is active as an anti-tumor agent in glioblastoma xenograftsexpressing Δ2-7EGFR or carcinomas which overexpress the wtEGFR (22; 41;42). It was postulated that this antibody selectively recognizes anactivated form of the receptor (43). Studies on the isolated ECD of theEGFR have shown that mAb806 reacts with the surface-immmobilizedC-terminally truncated form of the ECD (aa 1-501) which lacks the CR2domain, but not with an N-terminally truncated form (aa 303-621),suggesting that the epitope is located towards the C-terminal part ofthe CR1 domain (Johns et al, manuscript submitted). mAb806 reacts weaklywith the surface of BaF/3 cells expressing ˜40,000 wtEGFR/cell, howeverBaF/3 cells expressing a similar number of the Δ2-7 receptors (whichlack L1 and most of the CR1 domains) bind mAb806 strongly (FIG. 16).Intriguingly, the ΔCR1 loop mutant (which lacks aa 244-259: (4)) hasstrong mAb806 reactivity. Assuming that mAb528 can recognize all thecorrectly folded EGFR on the cell surface, using FACS analysis it ispossible to determine the proportion of EGFRs reactive with mAb806 bycalculating the ratio in median fluorescence of mAb806 to mAb528: adirect comparison is possible because we use both antibodies atsaturating concentrations, binding is detected by the same secondaryantibody (Alexa 488-coupled anti-mouse Ig) and FACS detection is linearin the range used. Using this analysis, the proportion of receptorsreactive with mAb806 varies from 6-8% for the wtEGFR to 70-90% for theΔ2-7 and ΔCR1 loop EGFR (ratios of mAb806 to mAb528 binding of 0.06-0.08and 0.069-0.98: FIG. 14 and data not shown). Taken together, the datafor the isolated ECD and for the cellular receptors suggest that theepitope resides in the most C-terminal part of the CR1 domain and may bemasked by the native conformation of the wt receptor, but exposed bydeletion of the CR1-loop. Indeed, mapping of the mAb806 epitope onto thecrystal structure of the EGFR-ECD shows that it is located immediatelyC-terminal of the CR1-loop (see FIG. 9B,9C): thus the mAb806 epitope islikely to be buried at the CR1/CR1 interface in the back-to-back dimerform. The mAb806 epitope would also be partially buried in the tetheredform of the receptor. Only in the putative “intermediate”, untetheredform of the receptor, where it is not masked by CR1-loop/CR2 or CR1/CR1loops interactions, is the mAb806 epitope likely to be available. Thisantibody therefore could provide a sensitive conformational probe foranalyzing tethered, untethered and fully active EGFR complexes. To testthis hypothesis, we have monitored the reactivity of mAb806 with cellsexpressing wtEGFR before and after preincubation with mAb806 or withEGF. If mAb806 recognizes the intermediate form of the receptor, and theintermediate form is in dynamic equilibrium with the tethered(CR1-loop/CR2) and the CR1/CR1 untethered states, preincubation with theantibody should shift the equilibrium towards this species and henceincrease reactivity. Incubation with EGF, by favoring the formation ofthe CR1/CR1 interface, should decrease reactivity. wtEGFR/Baf cells wereexposed to mAb806 in the presence of the internalization inhibitorphenylarsine oxide (29) at 37° C. (to maximize the energy of thesystem), or to EGF at 4° to allow formation of the kinase active statebut completely exclude internalization. mAb806 treatment did not alterthe total number of EGFR (as determined by ¹²⁵I-EGF binding) and underboth conditions more than 95% of the EGFRs were present at the cellsurface (data not shown). After pre-treatment with mAb806, EGF orcontrol buffer, the wtEGFR reactivity with mAb528, mAb806 or controlantibodies was measured by FACS analysis. TABLE 5 shows the changes inmedian fluorescence channel caused by the pretreatment with mAb806 orEGF, as well as the ratios between mAb806 and 528 reactivity. Thismethod of presenting the data was chosen to overcome variations betweenexperiments in absolute median fluorescence values (which are verysensitive to small changes in the laser current and in the detectorsettings) and to allow pooling of the experimental data. Preincubationof the cells at 37° C. for one hour with 10 ug/ml of mAb806 more thandoubled the reactivity with mAb806 without affecting 528 reactivity;thus the ratio between the two antibodies was significantly elevated.Preincubation with mAb528 under identical conditions had no effect onsubsequent mAb528 or mAb806 binding (data not shown). In separateexperiments we proved that the enhanced mAb806 binding was notattributable to lack of saturation, since increasing the concentrationof mAb806 (from 10 μg/ml to 50 μg/ml) or the time of exposure (from 20minutes to 1 hr) during the second incubation had negligible effects(data not shown). The effect of pre-incubation with mAb806 was time- andtemperature dependent, reaching a maximum after 3 hrs preincubation at37° C. (data not shown). These results are compatible with trapping bymAb806 of a transient, untethered form of the EGFR receptor. Conversely,preincubation of the cells in EGF drastically decreases the reactivitywith mAb806. Internalization of the receptor under these conditions is<5%, hence cannot contribute significantly to the decrease in mAb806binding. In these experiments the reactivity with mAb528 also wasreduced by ˜20% after binding of EGF either through steric hindrance ormasking of the epitope. Taken together, these results point to selectiverecognition by mAb806 of an untethered, unligated form of the receptor.

TABLE 5 Variation in median fluorescence channel for wtEGFR-BaF/3 cellsupon preincubation with mAb806 or EGF Change (%) in antibody reactivityafter preincubation Probe with Preincubation: antibody: BuffermAb806^((a)) EGF^((b)) 528 — −3 +/− 2 −23 +/− 2  806 — +163 +/− 87  −48+/− 11 $\begin{matrix}{{Ratio} =} \\\frac{\text{(mAb806-control)}}{\text{(}\text{mAb528-control)}}\end{matrix}\quad$ 0.06 +/− 0.02 0.196 +/− 0.09 0.036 +/− 0.01 BaF/3cells expressing the wtEGFR were pre-incubated with control buffer, withmAb806 (10 μg/ml at 37° C. for 1 hr: (a)) or with EGF (10 ng/ml at 4° C.for 15 min (b)). Cells were then probed with either mAb806 or mAb528(both at 10 μg/ml) followed by Alexa488-labelled anti-mouse Ig asdescribed in Experimental Procedures. Cells were analysed on a FACScanand median fluorescence values obtained using the statistical analysisprogram in CellQuest. Median fluorescence values after mockpreincubation were 112 +/− 21 for mAb528, 7 +/− 1.9 for mAb806 and 0.5+/− 0.3 for the control (class matched) irrelevant antibody. Negativecontrol values were subtracted from all data. The results are presentedas positive or negative percent changes in median fluorescence for thetest samples compared to the mock samples. The ratios between medianfluorescence for mAb806 and for mAb528 are also presented. The data aremeans and standard errors of three separate experiments.

Analysis of mAb806 binding to the CR1-loop or CR2 mutants (TABLE 4)supports this: mAb806 reactivity was at least double that of wtEGFR inmutants with weakened CR1-loop/CR2 interaction (V⁵⁸³D and D⁵⁶³H), andaround three-fold higher than wtEGFR for receptors incapable of formingthe CR1/CR1 interaction (Y²⁴⁶ mutants). Incubation with EGF had oppositeeffects on the two classes of mutants: EGF reduced the reactivity withmAb806 of the receptors capable of forming the active dimer (wt and allof the CR2 mutants) while the reactivity with mAb806 was unchanged oreven enhanced for the CR1-loop mutants. The effect of EGF on thesemutants is consistent with an EGF-mediated untethering of a weakCR1-loop/CR2 loop interaction, accompanied by a failure to form theCR1/CR1 loops interaction. Modulation of mAb806 reactivity by EGFcorrelates well with the ability, or the failure, of the mutant EGFRs toactivate the EGFR kinase, as determined by tyrosine phosphorylation andby DNA incorporation (see FIG. 15 and TABLE 6). Our data are consistentwith a model in which mAb806 recognizes preferentially an untetheredform of the EGFR, which is yet to be configured unto the back-to-backdimer conformation. Thus mAb806 can be used as a tool to monitorconformational changes within the receptor upon ligand binding. Thetransient, untethered and unligated conformations of the EGFR wouldrepresent, at any one time, a small proportion of the total EGFRs butwould be present in detectable amounts on cells overexpressing thereceptor, as reported in the literature (22; 23; 30). Our data may alsohelp explain the ability of mAb806 to suppress tumor formation: in cellsexpressing the Δ2-7EGFR, binding of the antibody would sterically hinderformation of the kinase active conformation of the receptor complex,while in cells overexpressing the wtEGFR it may trap the untethered EGFRform and prevent interaction between the CR1-loops and consequentactivation. This hypothesis is consistent with the reported decrease inkinase activation of the Δ2-7 EGFR after treatment with mAb806 (42)

TABLE 6 mAb806 reactivity with cells expressing wt or mutant EGFR:changes in response to mAb806 or EGF. Ratio of mAb806 to mAb528 bindingin EGFR mutants relative to wtEGFR Preincubation : Cell lines BuffermAb806 EGF wt-EGFR 1 2.6 +/− 0.9 0.67 +/− 0.07 CR1 mutants: Y²⁴⁶F 2.9+/− 0.5 4.5 +/− 0.8 2.4 +/− 0.9 Y²⁴⁶W 3.2 +/− 0.5 3.8 +/− 0.7 5.7 +/−2.6 Y²⁴⁶D 3.0 +/− 0.5 5.6 +/− 0.57 3.8 +/− 1.4 CR2 mutants: V⁵⁸³D 2.2+/− 0.4 4.0 +/− 1.2 1.0 +/− 0.4 D⁵⁶³H 2.3 +/− 0.27 4.2 +/− 1 0.7 +/− 0.2E⁵⁷⁸C 1.3 +/− 0.4 2.8 +/− 1.2  1.1 +/− 0.05 BaF/3 cells expressing thewt or mutant EGFRs were processed as described in TABLE 3. The medianfluorescence values and the ratios between mAb806 and mAb528reactivities were calculated as described in TABLE 3. The ratio ofmAb806/mAb528 for the buffer-treated wtEGFR in each separate experimentwas taken as 1, and all other ratios were divided by the wtEGFR value toallow direct comparison between the mutants and between separateexperiments. The data are means and standard errors of at least fourseparate experiments.Conclusions

Mutations designed to test the role of the intra-receptor andinter-receptor tethers (4; 6; 9) in the context of the full-length,cellular EGFR indicate that: 1) The number of high-affinity EGF bindingsites is strongly affected by the CR1-loop/CR2 tether, presumablyreflecting the relative positioning of the L1 and L2 domains. Weakeningof the CR1/CR2 tether increases the proportion of high affinity sitesand strengthening the CR1-loop/CR2 tether abolishes high affinitybinding (TABLE 3). Notwithstanding the significant differences in ligandbinding affinities between the full-length cellular receptor and theisolated ECD, the CR1 and CR2 interactions drive the same relativechanges in the two molecules (cf. Ferguson et al., (9) and our data).Modulation of EGFR affinity by intracellular components (36; 44-46),which have been attributed to modification of the juxtamenbrane orkinase domains of the EGFR, must then reflect an altered balance betweentethered and untethered states. It is unclear how modifications of theintracellular portion of the EGFR leads to alterations in theconformation of the extracellular domain, and this will be aninteresting challenge for the future. 2) Ligand-independent dimerization(or oligomerization) of the EGFR is not significantly affected bymutations in the CR1-loop or CR2 domains. Weakening of the CR1-loop/CR2tether does not lead to constitutive dimerization, nor doesstrengthening of the tether decrease it (FIG. 12): thus, even when theCR1-loop is available for inter-receptor interactions (as suggested bythe mAb806 results in TABLE 4), productive dimerization and activation(assessed indirectly by phosphotyrosine content) do not occur withoutligand binding. However ligand-mediated EGFR dimerization and activationare affected by the mutation in the CR1 loop. These results indicatethat the constitutive and ligand induced dimers are not equivalent, andthat ligand binding is strictly required for the fine positioning of thereceptor subunits and consequent kinase activation (16). Tyr²⁴⁶ in theCR1-loop appears crucial for the formation of the activated complex.While it was formally possible that all mutations of Tyr²⁴⁶ locked thereceptor in the tethered conformation, our results obtained using theconformation-specific mAb806 (TABLE 6), point instead to an inability ofTyr²⁴⁶ mutants to orient the dimeric complex correctly. 3) We were ableto monitor significant changes in the conformation of the EGFR using anantibody, mAb806, which appears to recognize selectively the untetheredbut inactive form of the EGFR. Disruption of the CR1/CR2 interactionsincreases mAb806 reactivity, while ligand binding decreases it (TABLE6). Interestingly, both the D⁵⁶³H and V⁵⁸³D mutation and Y²⁴⁶ mutationsweaken CR1/CR2 interaction, leading to high reactivity with mAb806.Furthermore, the mutants with the mutations of Tyr²⁴⁶ most likely todisrupt the CR1/CR1 interaction (to trytophan and aspartic acid) show asignificant increase in mAb806 reactivity after EGF binding, confirmingthat the activated CR1/CR1 orientation is compromised. 4) Whenever theability to form an active dimer is maintained, the responses to EGF aredictated solely by the balance between affinity and receptor number. Wehave shown that, in BaF/3 cells expressing ligand-activatable EGFRs, asfew as 500 receptors/cell need to be occupied to stimulate half-maximalDNA synthesis (TABLE 4), and this correlates with threshold stimulationof downstream signaling effectors such as Shc and MAPK (FIG. 13). Thus,while EGFR phosphorylation itself continues to increase with receptoroccupancy (and hence ligand-dependent dimerization and activation), thesignaling pathways are fully activated at a much lower ligandconcentration; indeed, mitogenic stimulation occurs at concentrations ofEGF where phosphorylation of Shc and MAPK, but not EGFR phosphorylation,are easily detectable.

It is becoming clear that the EGFR can exist in multiple states, eachwith different ligand binding characteristics and potential foractivation by ligand: minor shifts in the equilibria between these formscan have significant repercussions for EGFR biology, particularlyconsidering how few receptors need to be activated to fully trigger thedownstream signaling cascades. We have summarized our understanding ofEGFR alternative conformations, and their role in receptor activation,in FIG. 17.

REFERENCES

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Example 3 Fine Epitope Mapping of Anti-Epidermal Growth Factor ReceptorAntibodies Through Random Mutagenesis and Yeast Surface Display

Fine epitope mapping of therapeutically relevant monoclonal antibodies(mAbs) to epidermal growth factor receptor (EGFR) was accomplishedthrough random mutagenesis and yeast surface display. A yeastsurface-displayed library of single point mutants of an EGFR ectodomainfragment (residues 273-621) was constructed by random mutagenesis, andthe library was sorted for reduced binding to a mAb of interest. If anEGFR mutant shows loss of binding to a mAb, this suggests that themutated residue is potentially a contact residue. Using this method, wehave identified key residues energetically important for the binding ofmAb 806 to EGFR. The mAb 806 epitope was localized to one face of theloop comprised of residues Cys287-Cys302, which is constrained by adisulfide bond and two salt bridges. The mAb 806 epitope as identifiedhere is not fully accessible in the autoinhibited EGFR monomerconformation, which is consistent with mAb 806 binding to a transitionalform of EGFR as it changes from an autoinhibited to extended monomer.

Introduction

Epitope mapping is the determination of antigen residues responsible formediatingantibody-antigen interactions. Previous methods of epitopemapping have involved expression of peptide fragments on the surface ofbacteriophage (1), Escherichia coli (2), or yeast (3), with subsequentantibody binding analysis. Mapping of antibody binding has also beenaccomplished through SPOT synthesis, where synthetic peptides arespotted on cellulose membranes and assayed for antibody binding (4).Phage display and SPOT techniques have been utilized to determine theepitopes of various antibodies against ErbB receptor family members (5,6, 7). However, peptide-based methods can only identify continuous,non-conformational epitopes. To identify a discontinuous epitope,H/D-exchange mass spectrometry has been used to localize an epitope todiscontinuous proteolytic fragments (8).

A useful tool in dissecting protein-protein interactions is alaninescanning, a method in which residues of interest are mutated to alanineand subsequent changes in binding are measured (9). This requiressoluble protein expression and characterization of each mutant to ensureproper folding. Shotgun scanning mutagenesis is a high-throughput methodof alanine scanning using phage display libraries and has been used forparatope mapping and mapping protein-protein interactions (10, 11).However, the non-eukaryotic expression system of this method may not beamenable to epitope mapping of complex eukaryotic glycoproteins such asthe epidermal growth factor receptor (EGFR) ectodomain, which contains25 disulfide bonds and 10 N-linked glycosylation sites (12).

EGFR is a 170 kDa transmembrane glycoprotein and receptor tyrosinekinase involved in the regulation of cell proliferation anddifferentiation (13, 14). EGFR (ErbB1, HER1) is a member of the ErbBreceptor family, which also includes ErbB2 (HER2, Neu), ErbB3 (HER3),and ErbB4 (HER4). A number of ligands, including epidermal growth factor(EGF) and transforming growth factor-α (TGF-α), bind to domains I andIII of the extracellular region to activate EGFR through dimerization.Domain II of the extracellular region is involved in mediatingdimerization contacts, and also forms an autoinhibitory contact withdomain IV in the monomer state (structures reviewed in (15)). EGFRoverexpression has been observed in a wide variety of malignancies,including head and neck, breast, bladder, prostate, kidney, andnon-small-cell lung cancers (16). This overexpression often correlateswith reduced survival rates and tumor recurrence and thus serves as apatient prognostic indicator (17). In addition, a mutant form of EGFRknown as EGFR vIII, in which amino acid residues 6-273 are deleted and anovel glycine is inserted at the junction, has been observed in cancerssuch as glioblastoma multiforme (18). Therefore, EGFR has emerged as animportant target for cancer therapy, and various antibodies that bind tothe EGFR extracellular domain have been developed to inhibit itsfunction.

MAb 806 is in preclinical development and has been shown topreferentially recognize vIII and amplified EGFR over wild-type EGFR(19; 22). It has been demonstrated that mAb 806 inhibits the growth oftumor xenografts expressing either vIII or amplified EGFR (23).

Recently, J. R. Cochran et al. reported a method for domain-levelepitope mapping using yeast surface displayed fragments of EGFR (27).Large fragments, some encompassing multiple domains of EGFR, wereexpressed and properly folded on the surface of yeast. These fragmentswere used to localize antibody binding to particular domains of EGFR forboth continuous and discontinuous epitopes. Yeast surface display is amethod whereby a protein of interest is expressed on the surface ofyeast as a fusion to the yeast Aga2 protein. The eukaryotic host resultsin transit of the protein through the yeast secretory pathway, allowingfor efficient disulfide isomerization and endoplasmic reticulum qualitycontrol (28). Yeast surface display has been used to affinity maturesingle-chain antibody fragments (29, 30) engineer protein stability andexpression (31, 32) and display a nonimmune human antibody library forscreening against a variety of antigens and haptens (33).

In the present work, we expand upon domain-level epitope mapping andutilize yeast surface display for finer, residue-level resolution ofantibody-antigen binding interactions. Previous work has shown that mAb806 binds to an epitope located in EGFR residues 273-621 (34). Startingwith this fragment, a yeast surface displayed library of single pointmutants of EGFR 273-621 was made using random mutagenesis. The librarywas sorted for loss of binding to mAb 806, and those clones weresequenced and analyzed. If an EGFR mutant displays loss of binding tomAb 806, this suggests that an antigen-antibody contact has been lost inthe mutation. Therefore, the mutated residue is possibly a contactresidue. Using this domain method, we have identified key residuesenergetically important for the binding of the therapeutically relevantmAb 806 to EGFR.

Results

Construction and Sorting of the Epitope Mapping Library

A fine epitope mapping library was constructed using low mutation rateerror-prone PCR random mutagenesis of EGFR fragment 273-621. Thefragment contained a C-terminal c-myc tag for detection of successfulEGFR mutant display on the yeast surface. The initial library size was5×10⁵ clones, and sequencing of 100 unselected clones indicated that 72%were wild-type EGFR, 17% single amino acid mutants, and 11% multiplemutations or frameshifts. This gives a relevant library size 8.5×10⁴,which is an order of magnitude higher than the largest theoreticaldiversity of single amino acid mutants of this 349 residue fragment(6.6×10³), and almost two orders of magnitude larger than the 1.0×10³possible single nucleotide mutations. Given this library size, everyamino acid accessible in the genetic code by a single nucleotidemutation should be well-represented in the library. The library wastransformed into yeast and induced to display the EGFR mutants on thecell surface as fusions to the yeast Aga2 protein. The library waslabeled with a high concentration of mAb, at least an order of magnitudehigher than the wild-type apparent dissociation constant, allowing fordifferentiation between wild-type binding and loss of affinity. Thecells were also labeled with chicken anti-c-myc IgY to detect EGFR273-621 expression. The mutants that were displayed on the surface ofyeast but showed loss of affinity to the mAb were isolated (FIG. 18A-B).It is expected that grossly misfolded mutants are recognized andretained by the secretory quality control apparatus (31; 35), resultingin significantly reduced cell surface c-myc immunofluorescence of thesemutants. After sufficient population enrichment was observed, singleEGFR mutant clones were sequenced and characterized.

Identification of the mAb 806 Epitope

For epitope mapping of mAb 806, the library was sorted at 10 nM 806 forsort 1 and 75 nM for sorts 2 and 3, with individual clone sequencingafter sorts 2 and 3. Out of 100 clones sequenced, roughly 20% containedmultiple mutations and were omitted from subsequent analysis. The singlemutants isolated from the library for loss of binding to mAb 806 areshown in the left column of TABLE 7. All mutations are localized to thedisulfide-bonded loop between cysteines 287 and 302, as has beenpreviously determined (34). However, residue-level resolution andfurther information about the mAb 806 epitope have been obtained usingthe present method. The mutants with loss of binding to mAb 806 showeither complete or partial loss of binding (FIG. 18B-C) when compared towild-type (FIG. 18D) at 75 nM 806. Mutants were scored according to thedegree of binding at 75 nM 806, with ++ indicating wild-type binding, +partial loss of binding, and complete loss of binding (TABLE 7, leftcolumn). To verify the results from the fine epitope mapping library,alanine scanning through site-directed mutagenesis (SDM) was performedon the entire loop 287-302 (TABLE 7, right column). All sites with lossof binding by alanine scanning (287, 293, 298, and 302) correspond tomutants isolated from the library. Conversely, sites with loss of mAbbinding only upon substitution of a residue other than alanine (D297Y,R300C, R300P, and K301E) are not identifiable by alanine scanning, yetclearly form an energetically important component of the mAb 806epitope. Since an average of 6-7 amino acid substitutions are accessibleby single nucleotide mutagenesis, a larger range of physicochemicaldiversity can be sampled compared to alanine scanning. Mutants withunaltered c-myc immunofluorescent labeling intensity but reduced mAb 806labeling at 75 nM can be inferred to have reduced affinity for theantibody. In order to quantitatively correlate mAb 806 labeling at 75 nMwith particular affinity constants, titrations on the surface of yeastwere performed on three EGFR fragments to determine the apparentdissociation constants of mAb 806 for wild-type 273-621 (++), C287R (+),and E293K (−). The results are shown in FIG. 19. The dissociationconstant of mAb 806 for yeast surface-displayed wild-type 273-621 is2.13 nM (68% confidence interval of 1.83-2.50 nM), which is consistentwith the affinity found by Scatchard analysis of mAb 806 binding tocells expressing EGFR vIII (19). The C287R substitution raises thisdissociation constant to 127 nM (68% confidence interval of 103-160 nM),which gives a ΔΔG value of +2.4 kcal/mol when compared to wild-type and,in alanine scanning terms, is an intermediate loss of binding (36). TheE293K substitution leads to a Kd value of at least 30 mM, correspondingto a ΔΔG of +5.7 kcal/mol, indicating a “hot spot” for binding. Theabove ΔΔG values demonstrate the relative energetic importance of thesemutations and can be used to roughly estimate the energetic importanceof other mutants based on their binding score (++, +, or −) at 75 nM806.

TABLE 7 806-binding mutations identified by random or site-directedmutagenesis Comparison of mutants isolated from library for loss ofbinding to mAb 806 and site-directed mutagenesis (SDM) in loop 287-302.EGFR EGFR Mutant mAb 806 Mutant mAb 806 (Library) Binding (SDM) BindingC287G, R, S, W, Y + C287A + G288A ++ A289K ++ D290A ++ S291A ++ Y292A ++E293D, G + E293A + E293K − M294A ++ E295A ++ E296A ++ D297Y + D297A ++G298D, S − G298A + V299A, K ++ V299D − R300C + R300A ++ R300P − K301E +K301A ++ C302F, R, Y + C302A − C302G, S − ++ indicates wild typebinding; +, intermediate binding; and −, binding equal to negativecontrol (see FIG. 18).The mAb 806 Epitope is Constrained

The residues identified as energetically important for mAb 806 bindingare shown in FIG. 20. These residues are clustered on one face of loop287-302, which indicates that this is the mAb 806 epitope.Interestingly, Val299 is located in the middle of these residues, butwas not identified in the library or alanine scan. Thus, V299K and V299Dsite-directed mutants were made, and although the epitope canaccommodate a lysine residue without effect, an aspartic acidsubstitution ablates detectable binding (TABLE 7). This furtherindicates that mAb 806 is likely to contact this face of loop 287-302.mAb 806 binds to heat and SDS-denatured EGFR (34), which would imply alinear epitope; however, the epitope is not entirely continuous insequence as demonstrated by the library analysis. This is explained byexamination of the structure of loop 287-302, which shows that the sidechain of Glu293 projects from one side of the loop to the other putativecontact face. The mAb 806 epitope is constrained by a disulfide bond andtwo salt bridges, Glu293-Arg300 and Asp297-Lys301 (FIG. 20C). All sixresidues involved in these constraints were isolated from the libraryfor loss of binding to mAb 806, highlighting the importance of theconstrained nature of the epitope. The cysteine at position 287tolerates a wide variety of substitutions that lead to an intermediateloss of binding (TABLE 7), indicating that its energetic contribution tothe epitope may arise more from constraining the loop rather thancontacting the antibody. However, the cysteine at position 302 may morelikely be a contact residue because it only tolerates substitutions tolarger residues with aromatic character. The mAb 806 epitope in contextof the autoinhibited EGFR monomer structure is shown in FIG. 20D. Itappears that an antibody binding site would be partially blocked fromthe epitope in this conformation, consistent with the observation thatmAb 806 does not bind soluble EGFR, but does bind to an “untethered”EGFR mutant perturbed away from the autoinhibited conformation (34).

Discussion

This work describes a novel method of fine epitope mapping usingscreening of randomly mutagenized antigen displayed on the yeast cellsurface. The method is able to identify nonlinear epitopes of antibodiesbinding to complex eukaryotic proteins without prior knowledge ofpotential contact residues. These are several advantages relative topeptide epitope mapping methods and alanine scanning. The yeast surfacedisplay platform facilitates protein expression, without the need tosolubly express and purify each individual mutant. Mutantcharacterization and titration are also efficiently carried out on thesurface of yeast. This method was able to definitively identify theepitope for mAb 806, whose epitope is not tertiary-structure dependent.Because of this, all single mutations isolated from the library for lossof binding to mAb 806 were localized to a single plausible antibodycontact surface.

Using this epitope mapping method, the epitope for mAb 806 was localizedto one face of the constrained disulfide loop 287-302, withAsp297-Cys302, Glu293, and possibly Cys287 acting as contact residues.Such a structural motif has previously been described as a cystinenoose, which is a disulfide-constrained, surface-exposed loop importantin binding specificity (37). Cystine nooses have also been identified asmajor antigenic epitopes on various proteins, including protein G ofbovine respiratory syncytial virus and measles virus hemagglutininprotein (38; 39). This suggests that a disulfide-constrained loop is afavorable antigenic structure; since it is already constrained, there isa smaller entropic cost upon antibody binding. Thus, a number of otherdisulfide loops on EGFR are potential epitope targets for antibodybinding. It has been shown that mAb 806 displays increased binding toEGFR on cells lacking the domain II dimerization arm. Therefore, it hasbeen hypothesized that mAb 806 binds to a transitional form of thereceptor as it changes from an autoinhibited to extended monomerconformation (see previous Examples and (34)). It is thought that uponmAb 806 binding, the EGFR monomer can no longer dimerize and activatethe receptor, accounting for its anti-tumor activity. The mAb 806epitope presented here is consistent with this hypothesis. The epitopeis only partially accessible in the autoinhibited monomer structure,with residues Glu293 and Cys392 obscured by adjacent domain II residues(FIG. 19D). These residues could become exposed upon a conformationaltransition and allow binding of mAb 806. The mAb 806 epitope of one EGFRmonomer is adjacent to the other monomer in the EGFR dimer structures,and antibody binding to this epitope could sterically prevent EGFRdimerization.

Materials and Methods

Construction and Expression of the Epitope Mapping Library

The epitope mapping library was constructed using the StratageneGeneMorph® random mutagenesis kit to give a low mutagenesis rate. Thetemplate used for library construction was a pCT302 backbone containingEGFR fragment 273-621, with a C283A mutation to prevent disulfidemispairing, inserted for yeast display (27). The PCR products were gelpurified and extracted using a Qiagen Qiaquick gel extraction kit. Thelibrary was transformed into Saccharomyces cerevisiae strain EBY100 (28)by electroporation (40) and homologous recombination (41) using aBio-Rad (Richmond, Calif.) Gene Pulser Transfection Apparatus. The finallibrary contained a roughly Poisson distribution of amino acid changesto the EGFR fragment as demonstrated by plasmid recovery using Zymoprep™(Zymo Research) and sequencing of 100 library clones (MIT BiopolymersLaboratory). Growth and expression of the library using yeast surfacedisplay was performed as previously described (28).

Labeling and Sorting of Library

The anti-human EGFR mouse monoclonal antibody 806 was generouslyprovided by the Ludwig Institute for Cancer Research. Anti-c-myc chickenIgY fraction was purchased from Molecular Probes (Eugene, Oreg.). Anappropriate number of yeast cells (at least 10× library size) werewashed with FACS buffer (phosphate buffered saline containing 1 mg/mlbovine serum albumin). The cells were incubated with 4 μg/ml anti-c-mycchicken IgY and the appropriate concentration of mAb for 30 min at 25°C. The cells were then washed with FACS buffer and incubated with 1:25dilution phycoerythrin-labeled goat anti-mouse IgG (Sigma) and 1:100dilution Alexa Fluor® 488 goat anti-chicken IgG (Molecular Probes) for30 min at 4° C. The labeled cells were rinsed, and cell libraries weresorted using a MoFlo FACS machine at the MIT flow cytometry corefacility.

Identification and Testing of Single Clones

Plasmids from the sorted library populations were recovered usingZymoprep™ and sequenced at the MIT Biopolymers Laboratory. Site-directedmutants were made using QuickChange® site-directed mutagenesis(Stratagene). Single clones were transformed into yeast using EZ YeastTransformation (Zymo Research) and grown in minimal media (yeastnitrogen base, casein hydrolysate, dextrose, and phosphate buffer pH7.4) overnight. Yeast surface protein expression was induced bytransferring to minimal media with galactose and incubating overnight.For each clone, 1×10⁶ cells were labeled as before with anti-c-mycchicken IgY, the appropriate mAb, and secondary fluorescent antibodies.Fluorescence data was obtained using a Coulter Epics XL flow cytometer(Beckman-Coulter) and was analyzed using DakoCytomation Summit™ software

Titration of EGFR Fragment Against mAb806

Cells were grown and induced as above. 1×10⁶ cells were labeled asbefore using the appropriate concentration of mAb 806, anti-c-mycchicken IgY, and secondary fluorescent antibodies. Fluorescence data ofc-myc positive yeast were obtained using a Coulter Epics XL flowcytometer and were normalized by maximal and minimal mean fluorescenceintensities. The binding interaction was assumed to be a single sitebinding model with no ligand depletion. Titration data was fit to theequation

$\begin{matrix}{f_{mAB} = \frac{\lbrack{mAB}\rbrack}{\lbrack{mAB}\rbrack + \kappa_{d}}} & \left\lbrack {{Eq}.\mspace{14mu} 1} \right\rbrack\end{matrix}$where fmAb is the fractional binding of mAb 806 to yeast-surfacedisplayed EGFR 273-621, [mAb] is the concentration of mAb 806, and Kd isthe apparent dissociation constant. A global fit of three data sets wasperformed using Microsoft Excel, and 68% confidence intervals werecalculated according to (42).Protein Images and Surface Area Calculations

All EGFR protein images were generated using PyMOL software (DeLanoScientific LLC, at pymol.org). The solvent accessible surface area ofeach residue of EGFR (PDB ID 1NQL) was calculated using Getarea 1.1(Sealy Center for Structural Biology, University of Texas MedicalBranch, at scsb.utmb.edu/cgi-bin/get_a_form.tcl). A water probe size of1.0 was used to allow for correct identification of EGF contact residuesas being on the surface. Residues with a value of 20 or above wereconsidered surface residues.

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This invention may be embodied in other forms or carried out in otherways without departing from the spirit or essential characteristicsthereof. The present disclosure is therefore to be considered as in allaspects illustrate and not restrictive, the scope of the invention beingindicated by the appended Claims, and all changes which come within themeaning and range of equivalency are intended to be embraced therein.

Various references are cited throughout this Specification, each ofwhich is incorporated herein by reference in its entirety.

1. A pharmaceutical composition comprising an EGF family receptorpeptide antibody specifically directed against the peptide of SEQ IDNO:1 and a pharmaceutically acceptable carrier, wherein said antibody isnot mAb806 and is generated using an immunogen comprising an EGFreceptor peptide selected from the group consisting of an EGF receptorpeptide of SEQ ID NO:1, and a variant or mutant of an EGF receptorpeptide of SEQ ID NO:1 having one or more amino acid substitutions andwhich is recognized or bound by mAb806, wherein said immunogen isoptionally conjugated to an immunogenic carrier.
 2. A purified antibodyspecifically directed against an EGF family receptor peptide of SEQ IDNO:1, wherein said antibody is not mAb806 and is generated using animmunogen comprising an EGF receptor peptide selected from the groupconsisting of an EGF receptor peptide of SEQ ID NO:1, and a variant ormutant of an EGF receptor peptide of SEQ ID NO:1 having one or moreamino acid substitutions and which is recognized or bound by mAb806,wherein said immunogen is optionally conjugated to an immunogeniccarrier.
 3. A purified antibody according to claim 2, wherein saidantibody is a monoclonal antibody.
 4. A purified antibody according toclaim 2, wherein said antibody is labeled with a detectable label.
 5. Apurified antibody according to claim 2, wherein said antibody is animmunoconjugate and is covalently attached to or conjugated with one ormore other molecules or agents having a therapeutic or diagnosticpurpose.
 6. A purified antibody according to claim 5, wherein said othermolecules or agents are selected from other antibodies or antibodyfragments which are not immunoreactive with an EGFR peptide of SEQ IDNO:1, toxins, ligands, radioactive isotopes and chemotherapeutic agents.7. A method for generating antibodies immunoreactive with an epitopeexposed on cells expressing abnormal or overexpressed EGFR, but notexposed on wild type cells, comprising immunizing an animal with an EGFreceptor peptide selected from the group consisting of an EGF receptorpeptide of SEQ ID NO:1, and a variant or mutant of an EGF receptorpeptide of SEQ ID NO:1 having one or more amino acid substitutions andwhich is recognized or bound by mAb806, and isolating peptide bindingantibodies.
 8. A method for selecting antibodies immunoreactive with anepitope exposed on cells expressing abnormal or overexpressed EGFR, butnot exposed on wild type cells, comprising screening candidateantibodies or cells expressing antibodies or active antibody fragmentswith an EGF receptor peptide of SEQ ID NO:1.
 9. A pharmaceuticalcomposition comprising an EGF family receptor peptide antibodyspecifically directed against the peptide of SEQ ID NO:1 and apharmaceutically acceptable carrier, wherein said antibody is not mAb806and is generated using an immunogen comprising an EGF receptor peptideconsisting of SEQ ID NO:1, wherein said immunogen is optionallyconjugated to an immunogenic carrier.
 10. A purified antibodyspecifically directed against an EGF family receptor peptide of SEQ IDNO:1, wherein said antibody is not mAb806 and is generated using animmunogen comprising an EGF receptor peptide consisting of SEQ ID NO:1,wherein said immunogen is optionally conjugated to an immunogeniccarrier.
 11. A purified antibody according to claim 10, wherein saidantibody is a monoclonal antibody.
 12. A purified antibody according toclaim 10, wherein said antibody is labeled with a detectable label. 13.A purified antibody according to claim 10, wherein said antibody is animmunoconjugate and is covalently attached to or conjugated with one ormore other molecules or agents having a therapeutic or diagnosticpurpose.
 14. A purified antibody according to claim 13, wherein saidother molecules or agents are selected from other antibodies or antibodyfragments which are not immunoreactive with an EGFR peptide of SEQ IDNO:1, toxins, ligands, radioactive isotopes and chemotherapeutic agents.15. A pharmaceutical composition comprising an EGF family receptorpeptide antibody specifically directed against the peptide of SEQ IDNO:1 and a pharmaceutically acceptable carrier, wherein said antibody isnot mAb806.
 16. A purified antibody specifically directed against an EGFfamily receptor peptide of SEQ ID NO:1, wherein said antibody is notmAB806.
 17. A purified antibody according to claim 16, wherein saidantibody is a monoclonal antibody.